If you have free play and 0 credits, that's the problem. You must have credits OR Free Play only. Make sure you have all balls loaded (required #)

Battery holder must have positive to the top of the board. Yes, that sounds like where the problem is coming from.
Check all solder joints, check components and make sure nothing got bent over, shorted and broken off.
Make darn sure you have the right connectors across the bottom of CPU board connected correctly.Use owners manual in rear to check connector number/wire colors to get the connectors right if you didn't mark them before original removal.
Make darn sure the ribbon cable from CPU to PD Board is connected correctly, be very careful on the pin alignment.

You could but you would have to change the main chip or it would not boot up correctly. Leave the original CPU in and remove the two bottom row connectors and power on, then start the top row left connector and install one at a time from left to right and see what happens.
There are many test you can do bit so hard to tell you by typing here. You need to follow the proper section of the Pinball repair guides.

So do you still get the fuses 115/115 warning? What other warning?