When you go into switch test and press the trough switch and ball switches, does it register the tilt and credit button as well? If so, you have some confusion in your switch matrix. Are no other switches causing double closures?

Something amiss with your switch column #1. This column includes Start button, Tilt, Left trough switch, Center trough switch, Right trough switch and Outhole switch. Check wiring (green with brown stripe) on each switch (J201-1) along with the associated diode on each switch. Make sure there is nothing metal touching the lugs of those switches that shouldn't be touching. Could also be something wrong with U20 on the CPU, but that would be the last thing I'd look at until all the easy stuff is gone through.

Have you done the previously suggested tests?

That sounds like crazy signal/logic stuff. I'd start by reseating all your ribbon cables in the backbox. Open it up and physically remove and reattach each cable, being careful to note that they're properly aligned upon reinstall.

Diodes rarely fail, the most common issues are that work was done on the game and a diode was reversed or the diode lead is bent and touching ground. Other than that there's really no reason to check them at this point since it is a pain as one lead has to be desoldered.

Go into switch edge test and close the outhole switch and see if the tilt switch (and possibly others) also indicate closed. Do the same for the drain switch.

As miguel351 said reseating the ribbon cables wouldn't be a bad idea.