Optos, Optos, Optos ...
Before you do any kind of crazy board work ... check and clean all optos. Especially the ones under the playfield in the underground tunnels. That area gets real dirty. In fact, make sure not to bypass cleaning the tunnels when you shop it out. To clean the optos, q-tips and isopropyl alchohol!
Also, your original trough boards may be just fine. Just inspect them for any disconnected or broken components (due to vibration). Also inspect for broken traces. If you are not comfortable with board work, you might want to find someone who can help you inspect them and test for continuity.
All it takes is one dirty opto ... or one disconnected (or cold soldered) component to give you plenty of ball trough issues.
Finally, always try re-seating ribbon cables on the main boards. Just make sure to reseat them the same way ... and be gentle ... not to break or bend any of those delicate pins.
Cheers