Sounds like a connector to the CPU board. Common issue if they are not repinned.

Yes, but looking at the schematic the trough switches are not all on the same strobe or return line, and he says the other switches are working fine?  The top lane switches are on the same strobe as the 4th and 5th ball trough switches, while the first in-line drop target and "4" target are on the same return as the 1st ball trough, 4th ball trough and end of trough switches, so check that these are all working.