Did you replace the MPU with an Alltek or just the LED on the original MPU? If the corresponding LED on the SBD is lighting up then I would think you have a connection issue. Since this game wasn't working when you got it, you don't know what other people have done to it and believe some people that shouldn't work on pins do and screw them up. Try following the wires from coil to coil. Look for bad solder connections on the coil lugs. Check for continuity on the common side of the coil to the other coils. Make sure none of the coils were wired backwards. This could break the flow of the daisy chain of the coil wiring.
The flippers are on a separate circuit and only work when the flipper relay is active(closed) and of course when the flipper buttons are pressed.