Go into the switch test on the diagnostics (Red button on the coindoor). Remove the ball from the machine, and make sure all the targets are up. The number of the closed switch will be in the credit display.
That's where I would start.
Clean and gap the trough switch - double check it is working in the diag by dropping the ball into the trough
Switch the machine off - refit all the MPU connectors.
Switch on and test.
