If your plan is to replace the LM339s, you're just digging a deeper hole, they're not bad. You took out traces/thru-holes when you replaced the bridges and caps (blanket replacement of these parts is ALWAYS unnecessary) and lost 12V for the switch matrix, and dedicated switches. That's my educated guess by your description anyway.
Measure all your voltages from the driver board, you'll likely find the switch matrix regulated 12V is now gone.
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Rob Anthony
Pinball Classics
http://LockWhenLit.com
Quality Board Work - In Home Service
borygard at gmail dot com