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FJR Project Bike Rebuild

33K views 113 replies 30 participants last post by  RaYzerman 
#1 ·
I have posted here and there hinting at this project, which deserves its own thread. The project is a 2006 FJR, 148k kms (90k miles), and essentially was delivered to me in a basket. I will post another thread of Forensic Analysis to explain what went wrong. Here is a few pics of the bike as it was disassembled at the dealer, then a pic of the complete bike as it was loaded (laying down) in my trailer.









Yes, it is all there, except the tires (new set the owner kept) and the battery. This sat in my trailer all summer and it's time to get it back together. The revised goal I have is to have it for sale next spring, so we have some time.....

First, have to get organized, get some tires on, install the wheels and some brake levers. So I got most of the boxes into the shop and got me a rolling chassis. This is how it looks now.




Engine parts boxes... there's more, but..... yikes!


To be continued, as you can imagine.........
 
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#33 · (Edited)
If you suspect the injectors, there is a really reasonably priced set of 2011 throttle bodies on Ebay right now. Which would also help the on/off throttle problem the 06's had.
 
#35 ·
Phil, a little FYI, the ECU would help the on/off throttle issue as FI programming was changed in '08, again '09 I believe. The throttle bodies themselves are pretty much the same, but changed with throttle by wire in 2013.
 
#34 ·
I'm such a tease.... those intakes were super clean for a reason. Here's a zoomed out view of the progress...... again look at those intakes, they seem to have a gold anodizing or something. But you can see this engine is getting ready to go, valves checked and all adjusted to exactly 70 percent of max. clearance. Another pic showing the cam sprocket timing marks when fully assembled.



 
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#37 ·
I'm not that far away from you and surely can help out. I'm "on call" for work next weekend and rarely get any calls and could help out. It would be really interesting to see one of these down to the nitty gritty and bits! If you have a Keurig coffee maker, I can bring K cups!
 
#38 ·
Phil, you may be right, the throttle effort was reduced from '08 on, whether it was lighter spring or different spring cam... I had not thought of that.. all good.


Coffee man, I love coffee. Keurig in the shop. Stay tuned.....
 
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#39 ·
Here is a pic of the engine, all ready to mount into the frame, however, I'm putting that on hold for a bit, as some frame cleanup must be done first. Valve cover on, starter installed, etc.







You should be asking or thinking something's wrong with these pictures.
 
#40 ·
I've been such a teaser and it's been fun, especially on the other forum where I had posted pictures of this engine a year ago, and of course nobody remembered. For those in the know, thanks for your support and playing along.

Did any of you notice the timing, clutch and stator covers were silver and not the darker gray of Gen2? I knew right from the get-go there was no way I would reassemble the '06 motor. Too much money involved for all the parts I'd need, etc. I stumbled on this Gen3 engine from a 2014 that got hit on the right rear, at alledgedly 13,000 miles, and bought it from a salvage outfit near Rome, NY. I paid a little extra, worth it, made a day drive, it jumped into my truck one year ago. However, as I was prepping this engine, I've determined there may have been a decimal place wrong in the mileage. More later.

The old engine will be put together one day without any new parts, call it a science project. Then I may donate it to the local high school for the younger folks to edumacate themselves, unless a better idea comes along. I'll document that later, and it should be a fun project.

So about that mileage..... I've already mentioned the intakes were squeaky clean and have what appears to be a gold anodizing on them (by Yamaha), which may have started with Gen3 as I've never seen that on a previous Gen. The exhausts have a wee bit of carbon. The exterior had very little dust/dirt. The timing cover and stator cover got some minor scars, I'd rather have the new covers left in place and not retrofit the dark gray ones. It will then be more obvious it's a new engine.

Someone here (dunno maybe) mentioned a new magnetic spark plug socket (Duralast) available at AutoZone ($6.99). Get one!! Love it. Thanks to whoever that was.....



So here are the spark plugs removed from that engine...... how many miles have they gone?? I'm pretty sure the answer is not 13,000 based on all the evidence.

 
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#41 ·
Time to move on to getting this bike together. To recap, the engine... after checking the parts catalog, I had to transfer some electrics from the '06 engine..... ignition pickup and trigger wheel are totally different on a Gen3 throttle by wire. Stator plug had been cut off, had to borrow the one from the '06 (same stator), neutral switch has a different connector so swapped it out, cylinder identification sensor and valve cover re-used from the '06, along with the coolant tube which is also different. Needed a starter (took apart '06, all was clean, and a bit cleaner now, so good to go). Oil level sensor different part number, but same connector, so leaving it alone. Removed some Lipstick Pink fairing paint residue from stator and timing covers. Engine sits awaiting frame cleanup......

Been multitasking on other non-m/c projects the whole time, but spent a few hours on the frame, cleaning off dust and dirt so she'll have clean underwear. Taking advantage of a lightweight engine-less frame to do chassis maintenance.... see my new lifting device, 2x4 just fits between wheel and swingarm, genius eh!. Removing centerstand, putting the bolts in the right way, fully serviced suspension pivot, removed swingarm and greased up the bearings, cleaned it all up while it was out, rear caliper apart to grease slides and clean up pads (almost new) so everything will work as it should, some new owner should be happy.





Swingarm has needle bearing on one side, sealed ball bearing on the other. I believe someone had been in here before as they used loctite on the nut where it doesn't call for it and duh, it is a locking nut, LOL. Had a heck of a time getting it loose (85 ft. lbs.). Did not feel I needed to do anything with the sealed bearing, actually everything was adequately lubed by whomever. I have also read those who did swingarm service found adequate grease from Yamaha. I think once you do it (to verify) and grease it, no need to go there again, it's quite robust.





Did some more cleanup and reassembled.







So there it is all shiny, all torques checked, time for an afternoon nap. Then I'll dig out the u-joint, grease up that driveshaft spline..... I decided to install the rear drive, wheel, etc. as I think I can slip the engine/u-joint on with everything in place. At least, I can't see why not.
 
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#42 ·
I spend a lot of time cleaning things up, going through my baskets and hardware collection, also taking time to do some maintenance. The rear brake pedal pivot was kinda sticky, so while this bike is in this state, best just take the whole darn thing off and do it right. See the red grease squeeze-out.
Also took the time to remove footpegs and clean off accumulated grunge, and since they were worn, put some new rubbers on... Gen3 rubbers I removed from mine, they are too mushy for my tastes, so they can go on here.



A bright spot in the boxes was this brand new left side footpeg stay, the old one had the front tab broken off, so I guess the PO decided to buy a new one (before they ruined his engine). My score, so cleaned up all the stuff off the old one, lubed the shift linkages, new rubbers here too.





Might as well service all the ground spiders while the engine is out of the way, got a couple up front to do yet, but that can wait. They were all dry and in good shape, but I scrubbed them a wee bit and coated them with contact paste. All healthy now.



 
#43 ·
I inspected the radiator assembly and it was obvious it needed a good cleaning. Accumulated bug guts, and a bit of road tar/tiny rocks stuck on the fins, otherwise seemed fine. Mostly it was in the bottom half dozen rows and some in the top few rows, expecially the last rows where there is little normal air flow. First recommendation, get a fender extender (I like that carbon fiber one from Spain that is a tad longer than most). I don't see the need for an aftermarket rad guard if you have a fender extender.

Removed horn, fans, rad guard. I started with a good spray of hydrogen peroxide to dissolve the organic matter (bug guts) and let it soak while I worked on other things. Then repeated, let sit. Blow it out from the back side, spray on some Simple Green (my new favourite cleaner), gentle scrubbing with toothbrush on all tanks, etc., let sit, rub into fins with a toothbrush, repeat, let sit, blow job, spray on some naptha to dissolve/soften the tarry stuff. Again repeating a couple of times, took a dental pick to dig out stuff. The fins are all in good shape, very few bent, no corrosion evident.

Next step was a trip to the laundry sink and applied dishwashing soap to all the fins, both sides, followed by a nice hot water rinse, surprising how much dirty water drained off. Rinsed again, let sit to let all the water drain out of the fins.... surprising how much water those fins hold. Rinsed the insides too, was clean. Maybe I was a bit anal about it, but the rad is a very important vital organ, worth all the effort since it was already out. Final step, back to the shop, spray with isopropanol, blow dry. I held it up to a 2000 lumen shop lite, took a couple of pics. Camera didn't like the light shining in its face, so hard to focus.





Reassembled rad guard, fans and horn.... ready for mounting into the bike at the appropriate time.



I spent probably half a day on this thing...... amongst other things of course, but on the rad cleaning itself a good two hours or more.
 
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#44 ·
Did the rad on my 84 GL1200. It took a month. I have a problem with "while I'm here" syndrome. I pulled the timing cover (swapping the timing belts) and a bunch of other stuff while I had the rad off. Once done, I even repainted the rad using a gloss black appliance epoxy paint. It looked great when done but it took a while. :grin2:
 
#46 ·
I'm a bit like Bounce, once it's apart, it's kinda like "Oh, should clean that up while I'm in here". Doubles or triples the "normal" time, it's one good reason this job is taking a while. I had budgeted 30 hours... yeah right. I listen to music in the shop too, here's a good one for that.......

 
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#47 ·
This is one of the things you've been waiting for....... finally decided to muscle a big piece of hardware. The new engine was on my hydraulic dirt bike lift, strapped on such that I could raise the lift and "walk" the beast over to a place right beside the main lift. Figured I could walk the engine off the lift onto a piece of plywood sitting atop my two scissor jacks, I'd slide it under the frame, knew I'd have to tilt it forward first..... get it slid in, tilt it back, jack it up. Genius, how hard could that be? And yes, I am doing this all by my lonesome. Guessing the engine weighs 200-250. I did kinda lift/walk it off my truck's tailgate onto the dirt bike lift a year ago, but no way I'll attempt to lift it now. So, a little creative and careful planning........ here we go, I can hear you now, OMG hold my beer watch this! Getting it onto the plywood/jacks was pretty simple.



Because of the steel plate on steel jacks, easy enough to slide it into place. Frame comes down at the front, so have to tilt the engine forward and lined up such that it will slide in sideways. Not enough clearance, so remove a jack, slide it under the suspension pivot, jack the frame up higher. Hmmm, can't get enough. With a little help from some 2 by pieces, ended up taking the other jack out so the only thing the engine sits on is the plywood. Still had some creative tilting and such, but it's lined up now.



Hint for you at home, if you're working alone, best not install the coolant pipe, as you'll need the room to tilt, etc. and the front tire gets in the way. Front wheel, BTW, is clamped into the lift so the lightweight frame won't move.



In case you're wondering, I was only wishing I could do it with that remote control, but alas, no ceiling hoist. With creative use of various wood pieces and a pry bar, jockeyed the engine up high enough to get a jack under it. Lift, tilt forward (with appropriate ratchet strap as safety from falling too far forward), slide back, etc. going from side to side. There's not a lot of side to side clearance inside that frame and everthing has to be lined up just right to get it such that I could put the rear lower engine mount bolt in, watching the middle gear u-joint guard doesn't get hung up.



Carefully jack it up, get one of the upper engine mount bolts in, go to the other side, line it up, put that one in. EZ PZ. Felt good.



This whole operation took about an hour and a half, including a few "let's think about this for a minute", get a coffee, hmmm, where does that wire go, and then just methodically make it happen. At no time was anything bad going to happen, now gimme back my beer! I thought I did pretty good for an old guy.

I spent a bit more time cleaning up the corrosion on the engine mount bolts, coating them with anti-seize and installing all bolts but the front lower ones where I will put the sliders back on. Best follow the order of loose install and tightening in the FSM, as mostly the left ones have to be done up first and the right ones have bushings with pinch bolts, self-seeking locations. The engine becomes part of the frame when it's all done up.

Note - Even with a helper, it is just way too finicky to attempt lining up the driveshaft and installing it as you go. Best leave that and final drive/rear wheel assembly until after the engine is in place. Lesson learned. However, I don't feel so bad as I have to remove the rear wheel again anyway to install that missing spacer.
 
#49 ·
You shoulda left the trannny output shaft out, mounted the engine, then see if it can be installed in place.
 
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#51 ·
Merit to that.... No need if you have a helper, but removing that metal shield on the middle gear woulda helped me. No need to remove the middle gear itself, but yes it can all be done while engine is in the bike.

Postoak, to unconfuse you, the certified mechanic story is true and that engine sits in pieces on the shelf for later assembly into a science project. Not worth spending a dime on, cuz the dimes add up to more than this new engine cost me. The new engine has very few miles on it, I'm going with 1,300 or so. It came out of a 2014 wreck, an incredible find really.
 
#52 ·
A niggling day today, maybe I'm getting PMS.......... But lemme 'splain that when you didn't take it apart, and it all arrives in "baskets", nothing labelled, parts in this box go with parts in that box, shuffle stuff around..... it also takes a bunch of extra time to watch out for electrical, what has to be done in what order, sort out the correct hardware to bolt things up, clean it up first if you have to. I'm sure you can imagine. I had gone through all the baskets, finally decided I was tired of going through baskets with hardware, just toss it all in one container or two. If you don't know what hardware goes where, don't worry about it. The beauty of the Yamaha parts numbering is you can in most cases identify the bolt/screw you need, just consult the parts manual for a particular item, keep your measuring scale handy. Glad it's not another brand for that reason alone. The good news is, I've taken FJR's apart, it helps for some things, but I've never been in this deep. Very fortunately, I've been able to find everything except one part so far. Here is my remaining hardware collection.......



You'll likely recognize some, frame sliders, T-bar bolts, various fairing fasteners. The baggies are mixed and some stuff in the bag doesn't go with that particular part, belongs to something else. The 8 internal hex nuts.. for the exhaust headers, but you can see the part I'm missing is one exhaust gasket. Headed to the local Yammy dealer today to get it, 'cuz I need the headers on real soon. And a little comment about the white container, yes indeed I do get some of my culture from yogurt containers!
 
#53 ·
Hardware and sorting out baskets is one thing, but let's talk electrical for a sec. Mainly the electrical that you have no clue about what the previous guy had done. I know he didn't do it himself, suspecting the Certified Yamaha mechanic had his fingers in it. When installilng the engine, wondered why there was this 10 ga. ground wire run down to attach where the factory ground attaches at the lower front of the engine. Followed it up, pulled it out, and here it is. At the top end is the 10 ga. with some smaller ground wires soldered to it, wonderful job (not up to JohnC standards nor mine), not wrapped up very well, nor is it what I would do... gee, the battery ground post was like 3" away, why not go there instead. Followed the trail to a relay tucked up into the mirror mount area, oh boy, big spade connectors and more "power" wires going somewhere into some convoluted harness wrapped up over the steering head to the other side. Followed some spaghetti... hmm looks like it powers the Fiamm Blaster horns, but there's more. In the harness I pulled out, there's a cluster of spade connectors, enough for a relay but relay gone. I know buddy had them remove some of his farkles to transfer to the new bike, so yeah, just snip, unplug and go, it's now my problem. I suspect that branch was for fork lights, which of course are gone. On the other side, a pair of spade connectors, presumably (for the moment) the light switch. Velcro on the handlebars, dunno what was attached there. Dunno how the horn switch is tied in, will have to verify. I can't do much up front right now because the wheel is chucked into the lift vise and I need to turn the handlebars side to side..... Later. I don't dare hook up a battery until this is taken care of. I have let the smoke out of stuff before, but mostly it was by accident. Besides, I don't see no fuses protecting this.







At the back end, found this tied into the rear tail light harness, ya gotta love white tape! Two little green wires snipped off, and a little box glued on to the rear fender piece. Looked again, dug into what the two branches of white tape were covering up... something snipped off. Brake light controller? Ah yes, memory coming back, I was later given the Hyperlites, found them in my own stash. Most likely will be removed and trashed. Dunno yet what those little green wires are for.





The horn wiring will be tested, the fork light crap removed also. The good news, it's the only add-on stuff I can find.
 
#54 ·
Man, what a nightmare! This very much reminds me of Hackaweek's 40 part youtube video series on overhauling a CB750 that came to him in boxes.
 
#55 ·
Well, it doesn't seem like a nightmare, just stay calm and figure out where stuff goes, and no pressure deadline.. Everything is kinda plug and play, just have to find the right hardware and take care of the PO's electrical crap, all will fall together. Hang in there, more good stuff coming.
 
#56 ·
Well, if you were observant, you may have noticed from the pics above that I got the radiator in. Sure could have used a helper, that thing was a bear. I couldn't install the headers because I'm missing a gasket (ordered, pick up Wednesday). But if you leave the lower rad mount undone, you can pull the bottom of the rad forward so you have plenty of room to get at header nuts. One piece I had to wrassle with is the big plastic air deflector that goes on behind the rad, up against the main wire harnesses at the front of the engine. So I engaged two helpers... one, a tie strap around the handlebars to keep that stiff old harness up so I didn't have to push against it much with the plastic piece.
Also found out this bike had the spider recall, which is why I couldn't find that particular spider. They plug a very robust harness into the spider, run it to the right side of the bike with an eyelet to attach to the negative batter terminal, and if that wasn't enough, they ran a thinner wire taped to the main ground wire going to the engine block (overkill). I unplugged it and greased it up with contact paste anyway. Got the stiff mass of harnesses up, such that I could "clip" the two ends of the deflector over the two mounting bosses, to which the rad's two upper mounts will bolt to. Tight here, the rad mounts need to be shoehorned into two slots for the brackets, push up and get the holes lined up. Easy to say, but try lifting the rad with one hand while you pry a bit here and there, and the opposite end of the rad wants to fall down. My second helper became doing up the upper rad hose on the left side so it could hold the rad up. A lot of wrassling still, spent way too much time on it. Eventually got it. No pics, wasn't in the mood, just happy it's in.

Did up the fan conections, horns, etc. while I dug into where this add-on horn relay wiring all goes. Bottom end OK, gotta work on cleaning things up at the battery end. Later. Got other stuff going on.
 
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#57 ·
Back to removing the back wheel again to install the spacer I found, and of course, to install the u-joint. Removed wheel and final drive. Check out the driveshaft splines, very little grease, it may have got some from the (suspected) swingarm bearing service someone may have done (remember the loctite on the right swingarm (locking) nut?). Initially I thought all the shiny spots were spline wear... cleaned it off and you can see the chatter marks from the original broaching/machining. Virtually no wear. Remember too that the final drive is spring loaded such that the driveshaft is always pushed forward fully engaged with the u-joint at all times regardless of swingarm travel, so no longtitudinal motion really takes place. U-joint can float a bit, but not worth talking about. Two pics, dirty and clean.





So here are the parts I have to install, u-joint goes through the plastic shield which is held on by a push pin (I have a stash from my automotive days), then the swingarm dust cover. All splines were given their light coating of moly paste, should never have to go here again for a very long time.





Back to the rear wheel spacer..... had a fine time removing the 3 screws that hold the cush drive cover on. Damaged the heads with my impact driver and JIS screwdriver, as they were very resistant. Hmm, red loctite... now it kicked in, I wasn't the one who was in there. Found the cush drive rubbers are virtually brand new, I know for sure it wasn't me now, and thinking back to when I thought I was, I remembered it was me working on my spare wheel for the other bike, not this one. Spacer was in the wheel, now what. Needle bearing and bushing in good shape, not dry, gave the needle bearing a nice coat of moly, installed the bushing and seal, wiped off the excess. Checked my spare parts stash for the 3 new screws, and wouldn't you know, I bought these a coupla years ago.







Rechecked parts diagram, then went to service manual, darn wouldn't you know the spacer gets inserted into the final drive, not the wheel. Duh!
OK, got the back end all buttoned up, she's ready for the road back there. Well, time to bolt on some new shiny bits, but first, let's clean up the side stand, all greasy and dirty. Notice the foam-backed foil piece on the back of the side stand switch..... heat shield. Very advisable to have it. Before and after cleanup.




Lookie there, nice new shiny footpeg stay all nicely torqued up and the shifter cam installed. Starting to look like a real motorcycle!
Old shifter rubber was worn down, way down... new one coming.

 
#59 ·
Long story... once the engine was out, the owner wanted his brand new tires off, I can't explain why the final drive was pulled, no need for that... I had offered the owner a new set of tires, but no, the bike was dismantled and if you look at post 1, you'll see how it got put on a skid. Carefully loaded it into my trailer, that was fun too. Lucky me, the mechanic moved very far away, because I might be up on charges of attempted .... never mind. I'm over it now. Comical in a way but sad.
 
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