Quoted from djriel:well the trough switch issue is probably either:
the switch isn't registering.
I believe this game has to have 6 balls in it. 1 less and it thinks a ball is still on the field.
Something in the wiring between those trough switches and the mpu.
mpu set incorrectly (alltek?)
something on the mpu flaking out.
6 balls in the game but only 5 in the trough. The other ball is the captive playfield ball in front of the inline drops.
If the trough switches all work in test then make sure they still active when you sit a ball on them (one switch at a time). Sometimes the arms on these micro switches need to be adjusted slightly. The switch maybe working but the ball isn't registering on it.