How to resurrect Yamaha FJR1300 that's been parked in my garage for 7 years?

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One spark plug cap/boot is being very difficult to remove. Any suggestions?
Pry up the edges of the boot with a flat bladed screwdriver. Rather than a penetrant, I would use a bit of spray silicone lube. (Penetrating oil may damage the rubber.) The rubber sometimes sticks to the metal after a bunch of heat cycles. To prevent future problems, smear a thin layer of silicone grease on the rubber where it meets metal. Same with the headlight boots - a thin smear of silicone grease makes future removal easy.
 
Spark plug pliers would have helped a lot. The plug wire pulled out of the boot and is corroded. I know yamaha shows this as an assembly with the coil. Is there a simple fix? Can the wires be replaced independent of the coils?
 

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See the post above about removing the boot. After liftint the edges, you may have to do a little prying and adding silicone spray lube. With respect to the wire, you can try trimming a bit off the end (maybe 1/4"). Once you get the boot out, you will see what appears to be a threaded spike. The boot get screwed back onto the wire with the "spike" making the contact.
 
Still plug wire pliers. Then once you get the boot out you can trim back the insulation 1/4 inch and reconnect it to the plug clip that is in the boot.

In absence of plug wire pliers, needle nose will work now that you already screwed up the actual wire.
 
Still plug wire pliers. Then once you get the boot out you can trim back the insulation 1/4 inch and reconnect it to the plug clip that is in the boot.

In absence of plug wire pliers, needle nose will work now that you already screwed up the actual wire.
See the post above about removing the boot. After liftint the edges, you may have to do a little prying and adding silicone spray lube. With respect to the wire, you can try trimming a bit off the end (maybe 1/4"). Once you get the boot out, you will see what appears to be a threaded spike. The boot get screwed back onto the wire with the "spike" making the contact.
Excellent. Thanks for the advice.
 
Spark plug pliers would have helped a lot. The plug wire pulled out of the boot and is corroded. I know yamaha shows this as an assembly with the coil. Is there a simple fix? Can the wires be replaced independent of the coils?

While you have the plug boot off the wire, use a volt / ohm meter to check the resistance in the boot.
There is a resister in the boot. The resistance should be in the neighborhood of 10K ohms.
If significantly different look into the spark plug end and see a screwdriver slotted retainer.
Unscrew that and a spring and the resistor will come out.
Clean up all the contact surfaces and the inside of the boot, then reassemble and check resistance again.
If you find that boot out of spec, it might be worth checking the others.

After 7 years, don't get in such a hurry that resurrection may be delayed further by damaging anything unnecessarily.
Be patient, don't lose focus and don't throw anything, you'll get there.

dan
 
While you have the plug boot off the wire, use a volt / ohm meter to check the resistance in the boot.
There is a resister in the boot. The resistance should be in the neighborhood of 10K ohms.
If significantly different look into the spark plug end and see a screwdriver slotted retainer.
Unscrew that and a spring and the resistor will come out.
Clean up all the contact surfaces and the inside of the boot, then reassemble and check resistance again.
If you find that boot out of spec, it might be worth checking the others.

After 7 years, don't get in such a hurry that resurrection may be delayed further by damaging anything unnecessarily.
Be patient, don't lose focus and don't throw anything, you'll get there.

dan
More good advice dan. I've been working carefully and diligently. I'll perform the inspection you recommend and report back.
 
I would keep it simple. Drain the fuel with a siphon pump and put in fresh fuel. Make sure the tires are not cracked, then I'd fire it up and see how it goes and stops. Once you know it's good to go, then the normal maintenance items should be attended to.
I did even less when reviving an 07 R6S that had been idle in a garage for nearly 10 years. It started right up with a new battery and I just burned through the old gas (ran much better with fresh gas). I even tiptoed around on 10 year old tires for awhile while getting used to the bike. New battery, fresh fluids and gas, new set of tires, and the bike is a sweet runner! Modern Yamahas rock and I’m sure yours will too!
 
I resurrected a low mileage 2006 FJR I bought at an estate sale last year. It sat through a winter in an open shed for an entire Iowa winter. Here are some of the things I found and addressed. Critters built nest in the air box...inspect your air box and change filter. Changed the dark brake and clutch fluid. If your bike has ABS, assume the ABS no longer works until you verify with test harness jumper procedure. Change shaft drive oil. Clean the front fork seals. Run a bottle of Yamaha Ring Free fuel additive through the system at double strength. Changed the oil when I got it, again at 50 miles, again in 200 miles, and every 2000 miles since. Synchronized throttle bodies. Changed tires. Used PlastiX on gauge faces. Changed wind screen. Follow-up with dealer about factory recalls on wiring harness and ignition switch. Replaced coolant with YamaCool (checked all cooling connections for corrosion/weakness). Clean and lubricate shift and brake lever bearing sleeves. It purrs like a dream now. I will be pulling the rear swing arm to lubricate bearings and replace as needed this winter (sooner if needed).
 
While you have the plug boot off the wire, use a volt / ohm meter to check the resistance in the boot.
There is a resister in the boot. The resistance should be in the neighborhood of 10K ohms.
If significantly different look into the spark plug end and see a screwdriver slotted retainer.
Unscrew that and a spring and the resistor will come out.
Clean up all the contact surfaces and the inside of the boot, then reassemble and check resistance again.
If you find that boot out of spec, it might be worth checking the others.

After 7 years, don't get in such a hurry that resurrection may be delayed further by damaging anything unnecessarily.
Be patient, don't lose focus and don't throw anything, you'll get there.

dan

The contact resistance was 990K ohms, but the contact where the where the wire goes is nasty looking and green. This makes sense since the end of the wire is also corroded and green.

Does the boot come apart further or should I just put in contact cleaner and swish it around with a small brush?

Also, after cutting the wire 1/4", I'm surprised that there's only 2 strands of wire. It also appears that the shop I've been taking my bike to for tune-ups and 2 valve clearance adjustments has cut the wire from the coil enough that it's too short. Does anyone know where I can source this wire and how to replace it?
 

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The wires are part of coil. No way that I am aware of to replace.
 
The wires are part of coil. No way that I am aware of to replace.
I read here that member radog said this is not a problem. I'll try and send him a pm.

PM says he's not a member. Maybe on another forum; time to search.

I'm thinking of doing the coil-on-cap mod described on this forum.
 
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I read here that member radog said this is not a problem. I'll try and send him a pm.

PM says he's not a member. Maybe on another forum; time to search.

I'm thinking of doing the coil-on-cap mod described on this forum.
Before getting too carried away with mods, maybe get it running and see if you will actually ride it. Used coil off eBay would fix your current issue cheaply.
 
I buttoned up the coil wiring for now.
I've also changed the oil & filter, changed the gear oil in the pumpkin and I'm currently working on flushing the radiator prior to engine start attempt and the radiator reservoir is full of gunk.

I've sprayed inside the reservoir with contact cleaner but the bottom of the reservoir is still full of gunk. I also tried using small piece of tissue and it's not coming out.

Anybody have any ideas on how to clean this or am I being too anal?
 

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Might need some acid or even toilet bowl cleaner. Wouldn't worry too much about it. CAREFULLY check the overflow tank for cracks and possible brittleness. This was fairly common in early Gen II. My '07 developed a slow leak and when I squeezed it, the thing actually broke.
 
I buttoned up the coil wiring for now.
I've also changed the oil & filter, changed the gear oil in the pumpkin and I'm currently working on flushing the radiator prior to engine start attempt and the radiator reservoir is full of gunk.

I've sprayed inside the reservoir with contact cleaner but the bottom of the reservoir is still full of gunk. I also tried using small piece of tissue and it's not coming out.

Anybody have any ideas on how to clean this or am I being too anal?
Bottle brush works. I wouldn't worry too much about it though .
 
I have the bike ready for the test start: turn the key on, bike is a neutral, the fuel pump running then stops but I found an issue. The rear wheel doesn't spin. I grabbed the rear wheel when it was on the center stand and it just doesn't move.

I didn't try to start it. I'll check to see if the rear brake is the issue after lunch.

Any ideas? Let me know. Thanks.
 
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I have the bike ready for the test start: turn the key on, bike is a neutral, the fuel pump running then stops but I found an issue. The rear wheel doesn't spin. I grabbed the rear wheel when it was on the center stand and it just doesn't move.

I didn't try to start it.

Any ideas? Let me know. Thanks.
In neutral? Likely the clutch plates are a bit stuck and will likely break loose once you attempt to turn it over. You might take the bike off the stand, sit on the seat and rock it forward and back to break them loose. Worst case scenario is you may have to do a clutch soak but I'm betting it won't be needed. (Search clutch soak on this site.)
 

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