Rowan,
I would suggest visually inspecting the trough switches from the underside of the playfield - to ensure no wiring has come loose / broken.
Secondly, I would remove the apron and test each trough switch in test mode (ie switch edge test) to ensure that each trough switch is registering.
Let us know how you go! 
What Marty said, if all switches register then use a ball in the trough to test.Using a finger will sometimes activate a switch to the point that the circumference of a ball wont. May be as simple as bending the switch actuator arm. Good luck.
