I have a 1991 K100LT that recently underwent major surgery (my own fault). I accidentally tried to jump start it with the terminals connected in reverse (there was a trickle charge adapter with aligator clips that I assumed would go red to red with jumper cables, I was wrong). So my trickle charging adapter wires melted through because of too much current. The motorcycle battery died and there was a weird backfire that blew off the throttle body equalizer caps. So that started the surgery.
I have resolved all the problems apart one. If the bike idles for too long if you try to go it will go about 1/8 mile and then start to bog, then be fine again after a few hundred feet (if it doesn't die). It seems like it's either flooding or starving. This used to be much more prevalent, but it now only happens in first and second gear. There have been a few times when I let it idle for 5-10 minutes there comes a point where the idle noticeably decreases for a moment (30 seconds), then back up to normal (from an idle of 1300 to maybe 7-800 RPM and back).
Things I have done in the surgery:
New Spark Plugs
Cleaned Air Filter (K&N)
Cleaned injectors (and tested with a paper towel, nice cone shape spray)
Replaced the s shaped crank case hose
Ran for a mile without fuel filter, no change
Cleaned tank and fuel pump pre-filter
Checked all throttle body rubber for leaks
Checked air intake for obstruction
Oil and filter change
I haven't checked anything in the exhaust, but it feels like it's flowing fine out of the exhaust pipe. There was also once when I got finished with a 30 mile ride that I opened the gas cap and it looked like smoke was coming out (not steam, actual smoke). The fuel pump could have just gotten really hot because I was low on fuel or the pump could be going, I don't know. I really don't want to spend several hundred on a fuel pump if that's not going to help either.
I will try to take a video later today to show exactly what's going on, but it's really intermittent so I don't know that that will work.