The project sat for a couple years due to work and other projects.  I finally came back to it just recently.  The problem I thought was happening is apparently just how they work.  The other issue was with the monitor, and I overhauled the board.  The teenage boys are enjoying playing it, instead of Minecraft

What position should DS1 dip switches be in. All off or all on. What about SW3 bonusing if I'm setting up tito

Curious, Did you resolve the issue?

David,
The small circuit board underneath the coin comparitor is called the coin-in optics.
That board is what registers coins as credits back to the MPU.
You need to take it apart and expose the coin "encoder".

The coin "encoder" guide is a plastic piece that directs the coins as they fall thru between the optical light beams called the "ABC" optics.
If the encoder is too large, a quarter can miss one of the beams and coins falling thru get "eaten"....in other words, although being directed into the hopper bowl, they don't count towards crediting the machine.
The correct "encoder" guide is one that has sort of a plastic molded bend, to push the quarter towards the left, so the coin breaks the "B" light beam of the ABC optics.
If that plastic molded guide isn't there, then you have an encoder really made for much larger casino tokens.

UPADATE. i found out the board is a 755. I also removed the Vaarta Battery. But i have the little 3.6 battery attached to the back of the board. I am guessing the clear chip i need is not the 97 and 17 chips. Should i use  IVC224 & Key 0045 ?