I know you have checked and tried plus replaced a bunch of stuff. If the coil doesn't fix it, try unplugging the TPS
I have also heard of guys having problems with the plug wire, another coil will cure this in testing.
I know it's been apart and put back together but make sure the rubber connection from the head to carb is good, if needed remove the screw spacers on the clamps to tighten the bubber a little tighter. (No air leak)
I assume you have a stock hot start, verify it does close and seal, if it's for some reason a dubach or other aftermarket make sure it works proper.
I know also you had the carb apart, is it possible the slide plate is upside down? I know that it comes as it warms up but stranger things have happened. You may have fixed your real problem cleaning the accell pump and accidentally caused a new one.
I didn't see if you had a stock exhaust
or not, but if it has a spark arrester it may need to be cleaned, also make sure the muffler baffle hasn't broken and is somehow blocking the exhaust (mirror and flashlight).
Just a few more thoughts but hopefully the coil repairs it.