Unfortunately sounds like issues with the surface mount components on the PRISM. The surface mount leads expand and flex with thermal change. When the PRISM warms up marginal connections are lost and you get the craziness you're seeing.
It's likely repairable by very skilled hands and the proper equipment.
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Rob Anthony
Pinball Classics
http://LockWhenLit.com
Quality Board Work - In Home Service
borygard at gmail dot com