Can you power the suspect MPU in the working game? Sure, just plug in the bottom left connector only (J4) on the MPU.
No real need to do that though, the LED flash already tells you what's wrong. Two flashes indicates a bad RAM. Very likely battery leakage has damaged traces and components on the lower and lower left of the board.
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Rob Anthony
Pinball Classics
http://LockWhenLit.com
Quality Board Work - In Home Service
borygard at gmail dot com