Another "rough running" problem

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Denver FJR - It's the fuking battery. Been going through the same scenario. Try a good trickle and if that helps, it's the battery.
Similar but different. Make sure your battery terminals have good contact and are tight. Read this.
Good luck, keep us posted. ;)
Ding ding ding!!! :yahoo:

After stewing on this issue a bit I realized I was getting sidetracked with thoughts of puregas (gasoline ****?) and was ignoring past symptoms. The previous time I troubleshot issue, it appeared to be electrical related specifically to the coil that fed cylinders 2 & 3. At the time, tugging on the 12v wires feeding the coils appeared to resolve issue. Whatever I did I knew tugging on some cables wasn't going to be a permanent fix and sure enough a few weeks later symptoms slowly crept back in.

Today I decided to dig in on the wiring with the plan to check connections between battery and coils. Before tearing into wiring, ran some checks. Weather in Denver has been crap past couple weeks with snow and generally frickin' cold temps so hadn't been on a ride in while. Started bike and rough running problem was still present. Checked exhaust manifold temps with IR gun, the inner pipes were reading about 425 and outer pipes were around 380. Idle was also low, about 900 which has also been a symptom.

Checked voltage, with engine off and bike just coming off trickle charger battery was reporting about 13.2 volts. Started engine and saw about same voltage at idle but jumping up to low 14's at about 3k RPM. All seems good here, yes?

Started at top with battery, terminals were tight and looked fine with no sign of corrosion but in spirit of being complete decided to clean them up. Gave terminals a light cleaning with 350 grit sandpaper and reattached. Started up and viola'! Engine was smooth and idle back at 1100 RPM where it should be. Throttle response between idle and 2k is very smooth and all exhaust pipes are reading in the 380° range. Man... if I could only road test it!

 
Ok, so I, who also live in Denver btw, have been having the exact same problem. I would add one other thing which is that sometimes I have the problem where it feels like the engine is under more than normal load and even the tiniest change in throttle makes the bike ride like a bucking bronco. This would only get fixed after the bike warms up AND I pull over and turn the ignition off and then back on. I changed my battery (it was time anyway) and the problem went away for a few days. Then it came back. I got a trickle charger and put it on the battery every time I pull into the garage now and the problem has mostly gone away. I still have some idle roughness, but I think that's my idle speed which I need to set again. I don't know for sure if this was the solution because it's only been a couple of weeks and the problem is definitely much worse when it's cold in the mornings, which it now no longer is.

 
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