Using alligator clips, put one end on ground, and tap the metal tab on Q40 on the LDB - that should light up the Playfield Shoot Again lamp. This will verify your circuitry to the playfield. For the backbox, same thing, but Q3.
Not sure what to tell you about the game code not working. All I can suggest is to manually make the A & B lanes to light the extra ball to verify whether its working.