You will likely have to repin the connectors to the MPU if you have not, I have done this on several of this era machine and it solves flaky lights and timing issues, also, you will want to replace the caps on the driver board in the HV section, and adjust the voltage with the pot there if you have not done this (170v iirc?). Also, for these, ground mods on the driver board are a must and can prevent funky behavior later, all cheap fixes to make it a reliable machine...