Do the switches all show as on in Self Test even when the switch plug (P7) is removed?
If YES, then you have damage on the MPU - one common reason is someone mixed up the Solenoid (P8) and Switch (P7) plugs - this will severely damage the MPU. Doing that takes out about 8 to 10 TTL chips and takes an hour or so to fix. Mind you it could be as simple as U11 has failed - do you see activity on its outputs? If not are the inputs changing state?
If NO, then something is wrong with the switch wiring or similar. Did someone short the wiring harness? That would be unlikely though...
I have a bit of info on Atari pins here: http://flippers.com/atari_pin_service.html