I'll make a comment so you don't feel ignored! I'm working out the kinks on a 1963 Major League and am reading up on other peoples experiences. I mean if everything is where it's supposed to be how could it now work, right?
The replay unit that adds and subtracts credits, your saying if it was set for 10 plays manually, put a quarter in it (Should light up the game at that moment) it will take plays away? If you start a game does it add a credit or remove one. Almost sounds like it went to game over immediately but not if you can play it.
If it worked at the previous owners location and if the headbox was removed I'm going to suggest unplugging the molex connectors and take a wire brush to the male plugs, the female side I don't have a tool for cleaning the inside but between a wire brush and plugging and unplugging several times changes things from weird things like what your describing go away, and for me new anomalies like the target assembly lights stop working... etc.. etc. Just keep at it.
Also check the unit, Take the score assembly out of the machine, ensure the reel assemblies move freely when a coil plunger is pulled in.
Good luck with yours, mine isn't a two player so you probably have some extra relays but each coin switch has it's own relay, if any switch is too close or too far apart it changes everything.