Switch column (drive) circuit on the CPU board
The columns leave the board on CN8. The path back toward the processor runs through a 1k x 8 resistor network, the 2N3904 transistors Q48 to Q55, 1.5k resistors R98 to R105, the 4.7k x 8 network RA11, the 74LS244 at 8J and finally pins 10 to 17 of the 6821 PIA at 8H. The 1k network and the 2N3904s are the usual failures.
Systems
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Source: Repairing DataEast 1987 (Laser War) to Sega 1995 (Batman Forever), Part Three, Clay Harrell (pinrepair.com)