Any switch errors in the status report?
Go into switch test and load balls one at a time into the trough to verify that those are working. Load balls one at a time into No Way Out to see if those switches are all working. Use a ball to test the switches through the Spine Chiller to verify that nothing weird is happening (multiple switch closures).
The ball getting stuck after being ejected to the upper playfield is likely caused by a divot in the playfield where the ball hammers into it. I have the same problem on mine. I bought the Cliffy protector to resolve the problem, and will install it when I reassemble my game.