I find myself still chasing my own problem too. The thumper still occasionally gives a hick-up in relation to the flipper buttons...........strange that our problems are similar.
This past weekend - the thumper quit working entirely.
After an afternoon studying the board and checking the resistors, transistors, etc.....
I found the problem in the "ground" or return line which is common to a number of items. The way I found it was by physically chasing the "suspect" wire throughout the wiring harness to the point of fault. Took a lot less time than it sounds like.
Perhaps you have a solder blob shorting the wiring harness?? This thought is what led me to follow the wiring harness carefully. I was not being cautious while making other repairs under the playfield and had a splat or two.
The targets on my game share a common ground with the coils - flippers, gate, drop-target, etc.
Ground wiring had come loose and the wires had separated thereby opening the circuit. Why all of these items were not effected is beyond me. Some things still worked??
I'm considering just re-doing the entire string in sections as time allows. Grab the schematic and go point-to-point re-soldering connections and replacing the small caps and diodes at each target, coil, switch, etc. Simple work - cheap cost - time well spent IMO.
Edited to say: The thumper still gives the occasional hick-up during game play.
I will continue to follow this discussion to see if you turn anything up.