yep - i pretty much thought the same thing as you. i reseated everything i could think of - and yes i had just the day before rebuilt the flippers so have done some work underneath, moving the board next to them - which i think controls the motors for the creature. everything was working though....but....who knows?
there's a board (when raised) bottom left of the playfield which has a led which doesn't light - i haven't yet checked the manual, but is this an opto controller? and should the led be on?
i tried tracing the wires but couldn't find where they were going - i'll have another look tomorrow.
also i'll check the connectors you're talking about tomorrow. need to sleep on it.