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I have a 98 softail custom evo motor with mikuni carb. Yesterday on my way home from i almost made it back it started miss firing and popping like crazy. Pulled over checked the plugs they were fine threw a new set in anyway. Started it back up and same thing. Would idle fine but as soon as you hit the gas it pop like crazy walked the bike home started it up and it ran fine. Possible vapor lock? i was sitting in some heavy traffic for quite some time.
 

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I struggled for month chasing a similar issue on my 97. I added an inline fuel filter, guess I has some corrosion in the tank and it fixed all the issues. Cleaned out the carb too. Since it seemed to run fine when cold though, maybe not helpful.
 

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What you describe sounds more like an ignition problem that a fuel problem. Carefully check the entire ignitin system.
 

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Jeez I wonder how many miles are on this 21 year old Softail ?
 

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Look carefully at the ignition module, sitting in traffic a long time heats up everything, look for signs on melting or heat damage.
 

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I had that issue with my 1980 Narrow Glide: That damn near drove me nuts.
The guy i bought the bike from was about 6'8" @ 330 lbs. easy, My buck fifty azz was the difference.

Why, well:
The prior owner had removed the gauges. When he removed the Tachometer, he just cut the wire and let it go in the neck of the triple tree.. He was heavy enough that the bike didn't shake around much under him. My pencil frame well, the bike was, lets just say, not quite so stable. That wire would bounce around in the neck and ground out intermittently!

Wile stopped, there was no way in he** to get it to back fire. Rolling on California's cement freeways: It sounded like a rolling gun battle.
That was the most difficult troubleshooting that i have ever done. Not to mention it took months to find... Intermittent electric problems SUCK!

I'm sure this isn't any help to your backfiring problem. Just know it CAN be WORSE!
Look for stupid simple stuff first! (I lern't my lesson)...
 
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