Repinning the MPU connectors won't help. They're just sending binary data to the driver board, a weak connection won't affect the strength of the pulse. The MPU's coil pulse times are controlled by the zero crossing signal so it's not really possible for them to be off either. Manually shorting the transistors is not a good test since you can't control your timings. Repin the connector for the coil on the driver board, check connectors on the rectifier board, clean/replace the playfield coil fuse holder, etc