Once I finish the clear I change back the chips and boot the machine up. I get a 61 and then I hols down the reset button until 61-1 appears. Once that happens I turn the key one time. Then is goes blank and then shoots out the 65-1 error.
If what you've posted is accurate for the steps you've taken, you're missing a step. After you get the 61-1, you must close and fully latch the door, THEN turn the jackpot reset key once.
As far as as 65-1 error, the correct procedure is to open the door, press and hold the self test button for a couple of seconds, then release it -- the error should clear.
A list of common S+ error codes and their resolutions can be found here:
http://www.newlifegames.net/igterrors/Could it actually be the Game Eprom being bad?
A 65 error refers to the
EEPROM on the fixed motherboard, not an EPROM chip on your MPU board. Yes, it's possible that it's bad, but you'd typically get a 65-0 error in that case indicating that the EEPROM is bad.