2006 Gen II - runs rough between 2k and 3k RPM...unless cooling fans are running

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My bike was behaving the same as the OP’s. I posted above that I thought the issue was with mixture and some smart people posted that the issue was electrical. It wasn’t until after I read this thread and starting riding my own bike that I realized that I had exactly the same issues as the OP.

I have been digging into my bike, including some analysis of the MAP sensor voltage which was interesting but ultimately a dead end. The MAP sensor and tubing was fine. Thread here.

What I could see with the AT on my PCV was that the mixture would run rich before the fans came on, and then lean out by about 0.5:1 AF, which would result in smoother running. I also noticed that the bike was running very rich at idle (12:1) and I corrected this by putting negative numbers in the idle cells on the PCV.

Yesterday, I started working through the voltage. The charging is good, 14.1v at 3000rpm. The battery was resting at about 12.5v. Hmm, the bike has been run regularly, so I was a bit surprised it was so low. I took the battery out and placed it on my smart trickle charge where it showed about 50% charge.

I installed a Shorai battery that was sitting on the shelf. It’s a 22Ah that I got as a replacement from Shorai for free when the 18Ah one I originally purchased for my GSA wouldn’t start the bike in cold temps. I never installed the 22Ah on the BMW because I gave up on Shorai and installed an Odyssey instead. The 22Ah Shorai is slightly too big for the FJR battery tray and the posts are reversed but it fit well enough to run some tests.

I started the bike and let it warm up. After it came up to temp, the rough running was gone. It was smooth from idle to 3000rpm. I kept blipping until the fans came on and saw no difference in running.

To road test, I installed the 18AH Shorai that was so useless on my BMW whenever the temp got below 40*F (it started the FJR at 50*F no problem this morning). I took the FJR for a spin today and everything was smooth as silk. “Job done” as Edd China would say.

I did notice that my old battery sat at 50% on my Noco 1.1A smart charger for a very long time and then jumped from 75% to 100% very quickly. My Noco 7.5A charger showed it as having full charge all along. It was showing 12.8v after sitting overnight off the charger but I think something is not right with that battery. I might get a load tester on it just for interest’s sake.

I don't have much confidence in the 18Ah Shorai, so I guess it's time for a new battery.

 
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Nice that you fixed it. Did you happen to look at the MAP sensor voltage or Diag display after the fix?

Would be of value knowing if that was a symptom of the crappy battery voltage.

 
I'm pretty sure that the MAP sensor was correct - it was showing (within 2kPa) the ambient pressure at my local airport. I found an online calculator and entered my altitude, temperature and posted airport pressure and it came back with 89kPa (abs), while both of my sensors showed 87kPa. Since two of my three values were approximate and both sensors showed exactly the same value, I figured it was good enough. It might be worth checking it again with a known good battery and see if it is closer.

I suspect that the way the battery was reacting to the charger, the voltage was bouncing around, confusing the ECU. It also explains why the bike always ran great after a long run on the highway but would run like crap immediately after starting (hot or cold). I'm not sure why the fans running helped, but maybe the extra load calmed the voltage.

 
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