You have to be methodical to pin down the problem to where it really is. Moving the power board from the other machine was a very good idea / test. This should rule out the power board for now. Is there any apparent battery leakage damage on the CPU board ? If there is any corrosion around that area , it's the very first thing to take care of. If the board is clean , the next step is to disconnect as many things as possible to rule them out until you have the strict minimum to cause your issue. Then once you narrowed down the issue , if it's not a wiring issue (pinched wire somewhere maybe, after servicing, shorted diode somewhere, etc) then it's time to lookup on the board with the schematic the next component connected to the flipper buttons and investigate that.

Also , simple using a multi meter on the 5v cannot guarantee you that the 5v didn't drop. It can drop so fast and come back that your meter won't see the difference and won't have time to react and display accordingly.