I would check idc connectors. I had an intermittent connection that was causing the trough to send out two balls at the start of multiball. The idc with the problem was the large one in the middle of the cable that's comes from the 7 opto board (the board that the two trough boards cables go into. The cable that leaves the 7 opto board plugs into another cable that heads to the back box, it was this connector that had the issue. This connection is under the 1 Goal insert. That connection was hanging down and hitting the lockdown area so every time the playfield was pulled out, that connector got banged around. Took months to discover this.
For checking the trough idc's, you can go to single switch tests, select trough opto 1, and wiggle all the related idc's for the troughs. If you get lucky and find an intermittent break, you'll get that "ding" tone, a bit easier than trying to watch the screen. Then select trough opto 2 and repeat. Do all the Optos this way. I couldn't find my problem, replaced Optos etc. then happened to be in test on the right switch while working under the playfield, and then started hearing the "ding" sound, I was like, what the heck is that?