Great work-
The coggy thing is the score motor-
The screw you pulled from the bottom that has the sharp pointed tip is a lock screw for the flipper shaft- the other stuff might possibly be from stepper unit rivets or possibly a target on the playfield- but I would guess stepper units. I would look at those carefully to be sure you have contacts everywhere your supposed to- the game will absolutely not play correctly (but could be as subtle as a light not lighting or something like that) if you missing contacts anywhere.

Looking really good- congratulations on a great job saving that part of the game. And best wishes during your recovery from black lung