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Premium Member
2015 FJR-1300ESF
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711 Posts
I have a Power Commander V for sale, but I believe the wiring harness (plus O2 sensor box) is specific to the 2013-2015 models. Probably wouldn't work on a Gen I. Too bad. I believe the Power Commander "brain box" can be programmed with any map for any bike, it's just the physical connections that are particular to a make, model, and year.
 

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2003 Yamaha FJR1300
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34 Posts
Discussion Starter · #62 ·
I have a Power Commander V for sale, but I believe the wiring harness (plus O2 sensor box) is specific to the 2013-2015 models. Probably wouldn't work on a Gen I. Too bad. I believe the Power Commander "brain box" can be programmed with any map for any bike, it's just the physical connections that are particular to a make, model, and year.
Oh man!!! Eventually I will find one and MAYBE try it out. Until then once I get the bike up and running I will be more than happy with its performance.
 

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Premium Member
2006 FJR1300 AS - Orion The Hunter
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1,302 Posts
Billy, it is my understanding that removing the P.A.I.R. system will eliminate the "popping" upon deceleration. It will also clean up the top of the motor, for any top end work. You will not notice any improvement in performance, as I understand. This is my experience on my Gen II model.

I do not think that your bike will necessarily benefit from a Power Commander. These bikes are really tightly tuned, so based on my experience with my Gen II, I wouldn't bother.

Now, I would consider looking for the R-Gaza engine and luggage guards!

And since I had to replace my ignition coils anyway, I converted to the coil-over-plug mod. The cost ended up being about the same, but my Gen II looks more modern with the coils-over-plugs, and runs just as good, if not better than, the external coils!
 

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Premium Member
2006 FJR1300 AS - Orion The Hunter
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1,302 Posts
Wow! It went up?? Yeah, that really sounds like it is not a beneficial accessory!

I am getting about 45MPG now on my Gen II. That incorporates both mild and spirited riding!
 

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Premium Member
2015 FJR-1300ESF
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711 Posts
Pretty crazy huh? I first tried zeroing out the PCV's program. Then watched my mileage over the next few tanks.

Once I confirmed that the bike didn't perform any differently, aside from a small bump in fuel mileage, I took out the PCV. It doesn't seem to do much for a Gen III except waste some gas.

I'll allow that one might possibly see a measurable increase in horsepower on a dyno, but my "butt dyno" can't tell a diff.
 

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Premium Member
2006 FJR1300 AS - Orion The Hunter
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1,302 Posts
Yeah, Mamma Yamma got these rockets dialed in!!
 

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Premium Member
Versys 1000, VFR800
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11,621 Posts
The PAIR system is a passive flow of air drawn into the exhaust ports by outgoing exhaust suction, only on decel when the PAIR solenoid opens. If you remove it, simply no air gets into the exhaust to help burn unburned gasses..
BTW, down the road (every year), check those caps for heat and ozone deterioration, depending on the material they might start cracking.....
 

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2003 Yamaha FJR1300
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34 Posts
Discussion Starter · #69 ·
BTW, down the road (every year), check those caps for heat and ozone deterioration, depending on the material they might start cracking.....
Good stuff to know on the PAIR system, lots of reading and a few video's on the subject so still very much in the learning phase. Every spring it takes me about 2-3 days per M/C to go thru the checks to include removal of the fairings and checking the "hidden" items so the caps will be on the list.

DESSERTBIKE: Really interesting information on the PCV and how it performed on your ride, just one of those curious itches I would not mind to scratch but the more all of you guys are throwing my way the better educated I become on the FJR. Honestly just being able to turn the key, swing the leg over and pooter on down the road on this vehicle will make me forget about modifying anything, I'm just going to enjoy the ride.
 

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2003 Yamaha FJR1300
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34 Posts
Discussion Starter · #70 ·
Started into getting everything back together again, getting all of the parts together....
Machine Engineering Space Metal Auto part


Did notice something interesting with the idle control module, they were both slightly different, I went and crossed referenced the parts on 3 different web sites and it seems that the part is correct...Updated version perhaps? The fitment and function of the new module worked fine.
Light Auto part Metal Personal protective equipment Fashion accessory

Auto part Personal protective equipment Gas Metal Automotive wheel system


Intake with brand new tubes, boy were they snug, had to use silicon so they would slide easily on the intake.


Motor vehicle Automotive design Automotive fuel system Automotive air manifold Automotive exterior


Whilst everything was apart I did take all of the pins out on the male and female side, cleaned the contacts, dipped the pins in die-electric grease and re-assembled. I did have a 250W halogen lamp aimed at the connectors to soften them up prior to pulling them out.

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I should have taken dis assembly pictures of the fuel pump, as you guys can see one of the tubes is facing the wrong way, Oh well, easily correctable.

Helmet Gas Personal protective equipment Plastic Fashion accessory


5 Gallon container of Evap - O -Rust and of course the tank. This process for me took 2 days since I had to flip the tank on the other end to get both sides. The only leakage I had was thru the gas cap key hole, I shoved a little bit of oakem (fibrous strands) that expanded and sealed the hole. Had to use the cap since I did not have a plug that fit the cap side.

Gas Composite material Metal Aluminium Machine


My curiosity usually leads to things not good, the electrical tape on injector plug #3 (I think) was a little loose so I figured it should be replace, but alas upon removal I noticed the wire was frayed. Made a clean cut and broke out the soldering tools, unfortunately there is not much real estate in there and you will notice I had premature shrink tube effect there. I have some electrical gooey liquid tape and went ahead and applied that, wrapped the wire with regular electrical tape and called it a day.

Hood Motor vehicle Automotive tire Automotive design Automotive exterior

Bicycle tire Wood Automotive tire Bicycle handlebar Gas
 

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Premium Member
Versys 1000, VFR800
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11,621 Posts
Wow, you've been busy! Doing a great job, looks real good!
 

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Premium Member
2006 FJR1300 AS - Orion The Hunter
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1,302 Posts
Loving all the detail pictures!! Good work!!!

Also, good spot on the frayed wire!! And great job on the fix!!
 

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209 Posts
Excellent! I spent a lot of time with white vinegar trying to get all the rust out of my '04 tank. It got 90% better but never good enough. I used one gallon of Evap-O-Rust regularly rotating the tank and that did the trick. Good stuff! I put in a small amount of kerosene to coat the tank and prevent flash rust. When it's time I'll just fill the tank with gas not worrying about the trace kerosene coating the metal. Having trouble finding a cheap fuel pump on ebay. Years ago you could get those things for $40-$75 because they never fail. Not so anymore. They are pricey bastards! New one's have more than doubled in cost from several years ago also.

I recently gave my virgin '04 an oil change and final drive change. Soon hope to replace the coolant and the hydraulic fluids. Then send the injectors out. After that and finding a fuel pump I'll be good.
 

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Premium Member
Versys 1000, VFR800
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11,621 Posts
The VFR guys swear by Quantum pumps, there are cheaper Chinese ones..... try this for $70

 

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Registered
2003 Yamaha FJR1300
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34 Posts
Discussion Starter · #76 ·
Well another update, hoping the pics and stories help others as I continue documenting this.

The bolts on the bottom of the tank are all the ones on the left, the one damaged hole had to be enlarged and "blind" tapped into the existing metal. There was actually enough material there for me to work with (lucked out) and as you can see the screw on the right is slightly larger. I was worried once everything was all together that it may leak in that part but as of now the tank if full of fuel and no leaks have been noticed. I did purchase a rather pricey tube of loctite 518 to have on hand but did not need it.
Gas Household hardware Auto part Nickel Monochrome


I did re-adjust the orientation of the fuel nipple on the bottom of the fuel pump, just took my time disassembling the unit and went from there. I also ensured that it was actually pointing in the right direction prior to final assembly. Good pic of the gasket positioning as well, angled side away from the bottom.

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Well, initial start up was a bit rough, going thru adjustments of throttle, throttle cable, idle adjustment so on and so forth. I did take all of the vacuum tubes off and just went ahead and replaced all of them, it did improve a few things and got rid of the "14" code. I fiddled around with the TPS for a little bit and decided I wanted to try the older one. Easier said than done, the little bottom screw was terrible to get out and even worse to get back in, but I managed to get it done. I did purchase a new Gas pressure regulator and throttle sensor assembly and they should be here soon. I did not notice any difference in performance, so I put the new one back in.

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Once the new parts come in, I will probably do the SYNC and go from there.
 

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209 Posts
I hope you don't mind me piggybacking off your thread...........

I made some progress today. Replaced all the hydraulic fluids and coolant. I'm guessing there is a distinct possibility that all these fluids are original and 19 years old. Remember, this '04 FJR has 2,927 miles on it and last logged oil change and fueling is from 2010/2011.

The hydraulic fluids were brown but not as bad as I had feared. Interestingly, there was some fine sediment in the old fluid. On a very positive not, when I cycled the ABS pump it worked! I thought for sure it wouldn't work with old fluid sitting for so many years without use.

On the bad news side, the coolant came out rust colored. I've never seen coolant so nasty.
 

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2003 Yamaha FJR1300
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34 Posts
Discussion Starter · #78 ·
Well, I finally got the machine running after a bit of tweaking, disassembly, re-assembly, drinking fuel...yeah, dropping, wiping and many "sentence enhancing" words later. I spent 3 days trying to figure out why the bike would start and run but when you twist the throttle it would die. Pulled everything out to include all of the hoses and fuel injection system, sealed everything up only to have the same thing happen again....lets tear everything down again and see if I missed something. I checked all of the wiring to include the spiders, and everything looked OK. I walked away from this a few times to give it a break and come back with fresh brains. It was during that time I read an entry from a gentleman on another FJR forum and he went thru a discussion on fuel pump re-assembly. I have gotten to the point I can drain the fuel, take the tank off and pull the fuel pump out in 10 minutes. So I went ahead and pulled the fuel pump apart and low and behold the little o-ring and plastic cap thing located inside the pump were put together wrong. I got everything together, put fuel back in and started the engine and it fired right up!!

Even with hoses hanging, missing fairing pieces and the battery not being securely fastened to the bike (and no seat) I took the bike out for a 3 mile stretch, did I mention it was dark and 18 degrees. I was excited and cold, ran the bike hard, went way faster than I should have but the machine just kept wanting to go, pulled back in the garage, shut everything down and called it a night. The pictures below do not belong to me and were taken by the author of the article.
Gas Auto part Composite material Machine Metal
White Wood Automotive lighting Gadget Rectangle


I did end up replacing the fuel filter again and modified the plastic assembly that holds the fuel float and board so I can pull the whole unit out without pulling it apart in the tank. I can't believe that 3 days of torment and self-loathing were all due to a little Oring in the wrong position. Just have to do the throttle sync, put all of the fairings back on, fill the tank, treat the fuel and store the bike for the winter 😒. Well, at least I have something to look forward to.
 

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Premium Member
2015 FJR-1300ESF
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711 Posts
Is an inline fuel filter modification a thing that people do with FJRs?

It was a semi-popular mod in the Vstrom world. Did it on my 2007 DL1000. Worked great, and was far cheaper than paying for a whole new pump/filter assembly just because Suzuki decided to make the high pressure filter non-serviceable.
 
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