The 40 pin interconnect, female connectors and mpu chip have been replaced. Sound, switches and drop targets, Oh and playfield lights are affected. Pop bumpers, flippers and displays work great. It seems like it is trying to catch up with a huge lag at times when it get this away. I'm also using a capped power supply and sound card to rule those out too. What will cause the pin to become non responsive after it warms up?
I can turn the pin off, try again 15 minutes later and can play a game or more before getting pin gets warmed up again.

Thank you for the reply Chris, I checked the MPU board and found that all of the sockets have been replaced but I did find IC13 still had the RH type of socket. I replaced it and reinstalled the boards back into the pin. After a short period of time the pin started acting up again. This time I used a can of compressed air spraying it on difference chips with no luck until I sprayed IC13. Once I sprayed that chip the pin started acting normal. I believe that I have an extra chip laying around, so I will test with that chip and see if this fixes the problem.

Well, it's not as bad as it was, but it's still hesitating on scoring and sound effects.

Any other thoughts or ideas? Still have the same problem.

It turned out to be a bad crystal causing the slow motion effect.