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I have a 2008 that sat for the last four years. Here is what I did to get it started, in case it may help someone else out. I bought a new battery, but naturally it cranked, but did not start. So I figured the old fuel in the tank screwed everything up. So first thing I did was disconnected the gas line that goes to the fuel rail for the fuel injectors, turned the key, and no gas came out, so the fuel pump was toast. Fuel pump didn't make any noise. So I removed the gas with a cheap manual pump from harbor freight. I put a little bit of that gas in an empty plastic water bottle, and it basically looked like Coca Cola. Once I got all the gas out, i looked in the tank and it was nasty, no rust, but full of varnish. So I dumped a gallon of denatured alchohol in the tank, and left that in the tank over night, and swooshed it around every once in a while. Next day I sucked that alcohol out with the manual pump and put it back in the container it came in, in case I needed it again, since that stuff is 20 bucks a gallon. I rinsed the tank out with my garden hose until the water came out clear. I removed the fuel pump from the tank and it looked pretty nasty. I was just going to get a new fuel pump, until I found out they cost $500.00! So I figured I would try to fix it. I sprayed the crap out of it with carburetor cleaner and hit it with a tooth brush to get the varnish off. I figured out how to disassemble the fuel pump without breaking it, and got lucky since the whole thing is made out of plastic. I took off the little fuel pump motor and put 12 volts to it to see if it would spin. There is a filter screen on the bottom of it that tore off, so I have to get one of those screens. Anyway, I kept putting 12 volts to the pump and spraying it with the carb cleaner until it finally started spinning again. I used up the rest of the carb cleaner on the pump and blew threw every hole until I got it about as clean as I could get it.

So next step was to finish washing out the gas tank. With the fuel pump out, you can get your hand in there with a rag and clean and dry the tank. I installed the fuel pump back in the tank. Then I went out and bought 4 feet of fuel line. I put in one gallon of fresh fuel in the tank. I hooked up the 4 feet of fuel line to the output of the fuel pump on the bottom of the tank. I then sat the tank temporary on top of the bike, i plugged in the wiring harness to the tank. Ran the other end of the fuel line to an empty water bottle. I turned the key and the fuel pump started pumping gas into the water bottle. It was the nasty gas that was still in the fuel pump. It only pumps gas for a couple of seconds, so you have to keep turning the key off and on until clean gas came out. So the gas tank was good to go!

Now to the fuel injectors. I didn't want to pull the fuel rail off and take the fuel injectors out unless I had to. So I just unplugged each one. I applied 12 volts to the two prongs sticking out of the fuel injectors. I just used an old battery and a couple of wires. All four fuel injectors clicked, so I knew they where not frozen shut, but I did not know if they where clogged. So I rolled the dice and just wired them back up. If the bike didn't start, I would pull the injectors and try to clean them. So i disconnected the 4 feet of fuel line, and hooked up the fuel tank line to the fuel rail. The momment of truth came, time to see if the old girl will come back to life. I turned the key on, I heard the fuel pump come on, I hit the starter and she fired back up instantly like she used to! I let her warm up, revved her up a few times and she was back to normal. What a great feeling. Next I have to do the normal maintenance, but at least the hard part is done. I still have to order that little screen that goes on the bottom of the fuel pump inside the tank, so I have to take it back apart again, but that is no big deal. I'm just glad I got it started and running.
 

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Versys 1000, VFR800
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You can actually get an aftermarket pump kit that has the screens, may be able to buy just the screen.... it's just two little gears on the upper end that pump the fuel up through the motor (to cool it). Anyway good job.
 

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318 Posts
Yamaha does not list a fuel pump filter sock separately for the FJR. However, they do list separate filter socks for some of the ATVs.
Or, there is this
2003-2019 YAMAHA FJR1300 FUEL PUMP FILTER / STRAINER NEW | eBay
Or this
2PCS Gasoline Strainer Fuel Pump Filter For Yamaha motorcycle R1/R6 Yamaha FZ8 | eBay

While you have the fuel pump apart again is a good time to replace the fuel pressure regulator.
If you clean the old one up good enough, you might be able to see some numbers.
They might look like this 23280-22010.
You can get a replacement here
GT7610-463 Fuel Pressure Regulator Fits:Chevrolet Lexus Pontiac Scion & Toyota 601871710847 | eBay

Or here
Amazon.com: Fuel Injection Pressure Regulators,Fuel Pressure Regulator PR236 FP10280 23280-22010 Compatible with Prizm,Lexus ES330,ES350,Pontiac Vibe,Scion TC,XB,Toyota Avalon,Camry,Celica,Corolla : Automotive

Or dozens of other places ranging from $5 to $75.

If you should have to separate the fuel injectors from the fuel rail and throttle body, you will probably need new O-Rings and or base gaskets. I've never used this kit before, but Ray says it works for the FJR injectors. And the whole kit is cheaper than just one O-Ring and one base gasket from Yamaha.
FUEL INJECTOR REPAIR KIT O-RINGS FILTERS YAMAHA F150 OUTBOARD FOUR STROKE 150HP | eBay


dan

There is a thin line between fishing and just standing on the shore looking like an idiot. -- Steven Wright
 

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10' FJR 1300 A ABS
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59 Posts
A good fuel system cleaner is a great solution for removing "some " of the varnish in the injection system. It will take a few tanks. I got my 10' last September. Didn't know how long it hadn't been running but a couple tanks with some seafood and it made a great difference in the idle and at lower rpm.
Just my 2 bits.
 

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2006 FJR1300 AS - Orion The Hunter
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1,467 Posts
Good One, Robin! I thought the exact same thing!! Marylander's know the worth of Old Bay Seasoning!!

I am in Texas now, but use it on my French Fries!
 

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10' FJR 1300 A ABS
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59 Posts
Yuck yuck! This damn phone won't let me send SEA FOAM. I really do know how to spell it. 🥴.
I'm so glad to make more than just my self lol. Anyone else know of a better fuel system cleaner?
I also know that I will regret asking.
 

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Versys 1000, VFR800
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Seafoam is not really an injector cleaner, it's basically naptha and isopropanol...... slow acting solvent for gummy stuff and alcohol to take care of water. Makes a decent maintenance cleaner or if you have "bad gas".
A harsher injector cleaner for hard deposits is something like Berryman's B12 or Gumout Complete Fuel System cleaner.... likely contain naptha, but also contain harsher chemicals like benzine, PEA, etc. There are others... look up the MSDS and you'll see what's in them.
 
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