Do a jumper test on the switch matrix of the MPU. Dont have the manual handy, but it should identify the row and column connectors on the board. Pull the two connectors, and using a small jumper wire, jumper pin 1 of the row to each pin of the column, one at a time on the board connector pins. Do this in switch edge test mode. Follow along and see if every row/column combo corresponds correctly to the matrix. Then move to pin 2 and repeat and so on, until you test all 64 combos.
If they show up correctly, then it's a wiring or diode issue in the playfield. If they dont, then board issue.