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Yamaha FJR Motorcycle Forum

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My 2006 runs as described when the battery gets weak. The way I check for this is to leave it on the tender overnight and it will run perfectly first start in the morning. Then it will get worse as the bike sits. Changing to a new battery solves the issue (until the new one starts doing the same thing, sometimes in as little as a year). I switched to a lithium battery a few years ago (just because I had one on the shelf that fit) and haven't had the issue since. My hypothesis is that the voltage starts to jump around as the battery gets weak at low revs and causes the ECU to change mixture. New batteries can really be hit and miss these days, so if you buy one, get a brand name.

I also worked on a member's bike that had similar issues (but far worse, it was almost unrideable below 3k rpm) and we found after much searching that one cam was off a tooth. However, the previous owner had had a valve adjustment done right before selling it which doesn't sound like that could be your issue.
 
My 2006 runs as described when the battery gets weak. The way I check for this is to leave it on the tender overnight and it will run perfectly first start in the morning. Then it will get worse as the bike sits. Changing to a new battery solves the issue (until the new one starts doing the same thing, sometimes in as little as a year). I switched to a lithium battery a few years ago (just because I had one on the shelf that fit) and haven't had the issue since. My hypothesis is that the voltage starts to jump around as the battery gets weak at low revs and causes the ECU to change mixture. New batteries can really be hit and miss these days, so if you buy one, get a brand name.

I also worked on a member's bike that had similar issues (but far worse, it was almost unrideable below 3k rpm) and we found after much searching that one cam was off a tooth. However, the previous owner had had a valve adjustment done right before selling it which doesn't sound like that could be your issue.

Your battery shouldn't be getting weak in one year. Or two. Unless it is a POS battery. I suspect there is something wrong with your charging system. What volts is it at with engine running?
 
I would definitely start with the CA evap system. However, I am not convinced that is your problem.

In one of the other FJR sandboxes there has been a years long effort to fix a surging 2013 FJR. Recent success came with replacing the fuel pressure regulator located in the fuel pump.

Read all about it here: Clicky Thingy

Geez, what a saga! Better than a Clancy novel.
I'm working on removing the evap system, have cleaned out all the air lines (found them to be free and clear), have raised my idle a tad to 1150-1200 (can't get to precise by just using the tach), and will perform another TB Synch. Then I'll ride her and see. If its still there, I'll look for a used complete Fuel Pump Assy which would replace all of that.

Thanks for the link. I'll have to sign up over there.
 
Well, Thanks to SkooterG for taking the time to perform a tank swap, but that DIDN'T solve the problem. This would indicate its not the Fuel Pump or the FP Regulator. So not sure where to go from here.

Interesting thing we played with while there was related to the elec charging system. While I have a new Anti Gravity lithium battery, he made notice of the lack of charging voltage (I have a Datel meter wired to the battery. I haven't seen anything above 13.7 for years now, but while the static voltage of the new lithium was at 13.2 (according to the Datel), upon starting it would drop to 13.0 and 13.1.....which upon revving the motor, it would climb up, but the fact it dropped seemed odd. When riding, I usually see 13.6 or 13.7 but like I said, I haven't seen anything above that for probably 8 years. We started wondering if somehow this could be causing the situation.

So I certainly need to pursue the roadstercycle R/R connector cable upgrade to deal with the charging....but not sure this will cure the hesitation/stumble when accelerating.
 
Voltage just drop during starting is normal. my non-lithium battery often sees 14+ volts with the motor running at least according to the voltage meters I have on the system at large. so less than that does seem little low on a happy charging system
 
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So, an update.

The tank swap from SkooterG seemed to indicate it wasn't related to the fuel pump or fuel pump relay as it still exhibited signs during that test.

In talking with Jack at roadstercycles, he didn't think it was related to the charging situation, and to test that, he said to remove the headlight fuse and take it for a test ride. By removing the fuse, it was now charging at 14.2, and the condition still existed, so while I may have a charging deficiency, it does not appear this is causing the hiccup/stumble I'm experiencing.

So, finally got around to dive back in and check the ignition coils and spark plug boots. Everything checks out OK and is in spec (coil primary, secondary and boots were all within FSM stated values).........EXCEPT when pulling Cyl #3 boot, it was broke half way around and then broke totally off in my hands when I got it fully out.



The big question is whether this was cracked all along..........or did I do it when I changed plugs a couple months back and didn't notice it. The condition existed before I changed these and still existed afterward with no real change in severity so I'm hoping it was cracked all along which may have been causing the issue. With the amount of bend you have to apply to Cyl #3 boot when re-inserting, its hard to imagine I didn't notice........but I'll never know.

So, current pricing for a new boot seems to be around $100 (for ONE frigging boot!!). An interesting question when looking at the parts fiche....Do the wires come with the purchase of the Coils, or the boots? Both items are called "Assy" but its not clear which one includes the wires.

Regardless, I found a complete coil/wire/boot assembly on ebay for $50 so have purchased that. When that gets here, I'll just take one of the boots to replace my bad one and I'll trim my existing wires 1/4 inch and try that.

So, thats where I stand, we'll see what happens next week.
 
You (or a previous owner) didn't, by any chance, adjust the valves or anything that might cause the valve timing chain to skip a tooth? WBill
 
So, current pricing for a new boot seems to be around $100 (for ONE frigging boot!!). An interesting question when looking at the parts fiche....Do the wires come with the purchase of the Coils, or the boots? Both items are called "Assy" but its not clear which one includes the wires.
Coil has two wires attached. From what I can see, the boots are priced per each and not part of the coil/wire assembly.
 
You (or a previous owner) didn't, by any chance, adjust the valves or anything that might cause the valve timing chain to skip a tooth? WBill

No, valve adjustment at 36K was done by the dealer. I did change out the CCT but made sure nothing moved in that process.

Coil has two wires attached. From what I can see, the boots are priced per each and not part of the coil/wire assembly.

Yep, of course. Brain fade moment. Amazing how the cost of those boots has gone up. Some posts I've read from a couple years ago they were only $50 each.
 
Update.

Appears we have SUCCESS.

A half hour ride yesterday produced no indication with throttle response very linear and smooth.

So, what was the cause?

Considering how long I've been experiencing the issue, I would have to say primary cause was the spark plug wire connections in the boots getting worn out. I think it got worse due to the Cyl #3 boot being cracked/compromised, which I probably caused/made worse when I changed plugs a couple months back.

My recent work was to trim 1/8 inch off all the wires, and replace the Cyl #3 boot. I rerouted #3 wire so I could insert it easier without bending the crap out of the boot. With the AIS system removed, I was able to just route the wire around/under the coolant sensor as opposed to coming in/under the tube right at the hole. Did another TBS sync after all that and .........it seems to be fine. We'll see if it lasts.

So, spending $200 on a new TPS was the biggest unnecessary cost (anyone need a good TPS? :p )

Luckily I purchased a complete setup (coils/wires/boots) off ebay for only $50. I removed all the boots to do resistance checks and found a corroded pin inside one that broke off when removing the wire. I made sure I looked at all mine and cleaned them thoroughly. The other 3 in the spare set were all good so it was interesting that the corrosion in this one wire/boot was so bad.

Thanks for the help.
 
My recent work was to trim 1/8 inch off all the wires, and replace the Cyl #3 boot. I rerouted #3 wire so I could insert it easier without bending the crap out of the boot.
Routing of the plug wires is critical but even then, Yamaha saved something like $0.02 by being stingy with the plug wires. They saved another similar amount in the taillight wires. (I cussed them quite a bit when I had to change a brake light.)
 
I fixed my 2007 by installing a power commander and fiddling with the fueling map.
 
Routing of the plug wires is critical but even then, Yamaha saved something like $0.02 by being stingy with the plug wires. They saved another similar amount in the taillight wires. (I cussed them quite a bit when I had to change a brake light.)

Yeah, for a while I was thinking of taking the longer #1 wire from the spare set I bought and replacing the existing #3 but threading that through from the coil was going to be a hassle. The more I looked and fiddled with it, I found a routing that worked :)
 
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