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Intermittent sputtering problem

Hello,

I went through the forum to search for similar problems but had no luck so I figured just post the question about it.

I bought a 2000 FXST back in the later part of 2007. Well kept and clean. Bike ran fine until July of 08 when I had taken the baffles out of the V&H staggered pipes I have on the bike and a mechanic at a HD dealership tinkered with my air/fuel float in my carb (CV Carb), since then I have had issues with the bike.

Firstly, about a month after that I was riding and my engine light had come on but ran fine for about 5 miles. Stopped for about a half and hour then started heading back home when all of a sudden, the bike went into some sort of "limp home mode". I was able to keep going but I had to stay in the lower end of each gear. My friend (who builds customs) swore it was the ECM. So we switched it out for another (slightly used one) and it ran fine for the rest of the season.

Back in February, It was 60 degrees out and decided to go for a ride and right as I got on the highway and got to third gear, it backfired and did the same thing, engine light & limp home mode! So I turned around and took it home. My friend still swore it was the ECM that is giving me the problem, so I went and got a brand new one! Put it in the bike, and I rode around town with no problems (maybe a total of 15 miles). Then yesterday, we went out riding and everything was fine until I hit the 70 mile mark, it started doing the same (EDIT) thing!! Backfiring, sputtering, engine light came on and off like 4 times, so I slowed down and pulled over to tell on of the guys I was riding with the problem. Sat for maybe a minute (at idle), cranked the throttle twice and it sounded fine, started off again, and the bike ran good the rest of the way home.

Now, I definitely know its not the ECM! Its brand new and only has 77 miles on it. So, we're now trying to figure out what the problem is. Has anybody ran into this problem before or heard anything similar that can give a little insight or advice on what could it possibly be would be GREATLY appreciated!! The season just getting started and they're are some benefit rides coming up that I want to be part of!

Thanks in advance.

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The first time that I started having the sputtering problem, it was maybe a month or so after the mechanic had messed with it. It didn't happen right away.
 
The fuel in the tank is the first place I would start. Drain the tank and blow out the petcock and add fresh gas. Clean out the carb with the drain above too.
 
Should have said remove the tank and clean it out. It works better than just draining it. You can swish it around to get anything out that may be in there.
 
How do I retrieve the code? I think the engine light was just coming on because it though it was stalling. By the time I got it home it was running fine and the engine light was not on. Very confused about the problem.
 
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