http://www.flippers.info/system6repairpart4.asp
Sounds like you have a short in your driver board. Not many good ways to find it sadly. Probably one of the chips is bad, unless there's some bridged trace somewhere. Try just leaving it plugged in for a while and see if any parts get hot?
How are you 'connecting' the driver board? All connectors? Just interconnect?
Tried a test rom to confirm your MPU is fine?