I dropped the bike off a Laidlaws HD yesterday. I've had the bike at the dealer I purchased it from 3 times already for this problem and they couldn't fix it, so I figured I'd try a new dealer/mechanic. I got a call this morning from the service writer that they were able to read the trouble codes and the two biggest problems were that one of the connectors was filled with oil?!? and that some of the fuses had major corrosion/rust. They cleaned everything out and the tech rode the bike for 15 miles with no problems and the check engine light didn't come on. I'll get more details from him on which connector was filled with oil and which fuses were corroded when I pick up the bike.

The biggest problem though he said was that the original dealer did a horrible job tuning the bike with the Screaming Eagle Race Tuner. I remember when I had the bike tuned 2 years ago, the dealer said they did the best they could within the stupid strict California emissions guidelines. Anyways, he wanted me to bring back the SERT and he will have his tech do a better job tuning the bike, but by law, he'll have to stay within the CA guidelines. I dropped off the SERT today, but it won't get tuned until next Tuesday.

I know I've seen posts about this before, can a bike "fall out of tune" after a while? The bike ran great for about a year after the original tuning.

 

Moondogger - You might want to invest in a Go Pro helmet and try to capture it while it is happening.

 

UPDATE: I got the bike back about a week ago. It ran slightly better, but the hesitation was still there at times. Something that had been bothering me for a while was that the bike was always a little hard to start even though I kept it on a battery tender. I bought a new battery on Thursday and put it in the bike. When I test rode it after putting the new battery in, the bike ran like crap. Lurching, hesitating, and stalling. I barely made it around my neighborhood. All I could think was, "What did I fck up now??". I checked all the connections and everyting was nice and snug.

Today I decided to test ride the bike again. It started up fine and when I rode it, it was like a completely different bike. None of the hesitation was there. It ran like it was new. I've heard that an old battery could cause the problems I was having for the last year. I haven't changed since I bought the bike in 2009.

Now I'm wondering why the bike ran like crap right after I installed the new battery and why letting it sit for a day seemed to fix the problem???

 

I don't think it's the new battery. I say that based on it still having problems when you first installed the new battery. Intermittent problems are usually caused by something being loose. I hope the problem is gone. Chasing the tail of a mystery problem gets $$$$$.

 

I had two batteries with broken cell connections: all worked fine under light load except they refused to spin the starter motor.

According to our electrical diagram when the battery ground & 'clean' ground & battery '+' connection on the starter motor are OK then the electrical circuit 'deals' between the 40 Amp fuse and 'clean' ground. This means as soon as the generator provides power we mainly use the 'clean' ground and can live without the battery (above idling speed).

Once the engine runs, a faulty voltage regulator diode generates ripple and garbles the +12V line close to the ECU. Have you checked the condition of both connectors there? You can also disconnect your regulator and run only from the battery during your test.

 

I may be wrong but I think you hit the nail on the dead when you said ECM problem. It would cost you more money but you could install a Thundermax Tuner from Zippers and that may correct everything. Or may I suggest one more thing, cut your losses' and come to the realization that you may just have a lemon and trade up to a newer bike. Don't take me as being a smart azz because I'm not. Just looking at all your troubles and all the money you've already spent maybe it's time to just get rid of the ole girl.

 

Check and clean the terminals at the pcm and the throttle body. Use electrical cleaner then apply dielectric grease. More than likely a fretting problem.

 

The OP wrote his bike recently rode like new.
If the SE tuner works properly this means it is sufficiently well adapted to his engine. Do you think there could be an issue within the SE package?

 

Is it possible that because he had so many intermittent problems before changing batteries that the ECM had that "crap load" in it. Once the good battery took all the problems away, did the ECM need to run for a while to know that running properly was what it was supposed to do?

 

The ECM simply replies to solicitations (input signals) in a repeatable and orderly way. Its nothing more than an industrial programmable controller (PLC) adapted to our engine. What you call the "crap load" is immediately 'forgotten' and in the case of a Fuzzy Logic or calculated cycle normal operation will resume after a few thousand cycles / revolutions. This thing always falls on its feet as opposed to us