What is the shape of the 40 pin connector between the driver board and the MPU? Original?

With power off, try reseating all the connectors, including the 40 pin. I am assuming this is a problem that just started.

The all zeros is what a booting game does too. Your knocker and target reset probably have cooked transistors.

Check your power for blown fuses etc since you should have lamps too. You sure it's ball in play locked in and not game over? Ball in play stays on if your game is set to match off.

check Q19 transistor metal tab (5 bank targets) & Q41 transistor metal tab (credit knocker) for continuity to ground with a meter.

if you have continuity then the transistor is shorted internally and a possible reason these coils are locking on at power up.

check diode on Ball In Lamp.

No, there's no testing of the mpu board that would indicate 100% functional (bally/stern doesn't even do this with the bootup diagnostics - it can test the chips, etc. but it can't test the inputs/outputs of the PIAs, just the registers). If it boots up and runs software it's mostly working, and then you have to test outputs to see if any are stuck (logic probe best for this)

If the game wasn't booting the diagnostic routine wouldn't run anyway when you press the cpu board buttons.

It's not clear yet if your game is booting up, is it? Until it is, you can't depend on any signal being 'correct' as until it boots the PIAs are all in a random state. Remove the solenoid and lamp fuses until you are sure the game is booting if it's not.