A few easy things to try first:
- Check the board for any physical damage. Even the smallest scratch could mess things up for you
- Clean the Jamma edge connector
- pull the roms off, clean the legs, then re-seat them
- increase the voltage. sometimes these old boards just need a bit more juice to get them to play nice
- when running, try pushing down on some of the custom IC's and see if that changes anything. Also check to see if anything feels hot to the touch. Might help narrow some problems down
These are the low-hanging fruit things you can try, before having to dive into the schematics and logic probe stuff.