I would set it at exactly 5.0V measured with a load on (ie pcb attached). Better to measure on the pcb itself, any TTL IC will do (5V and GND pins).
If a board needs higher voltage it could be an issue with wiring that causes voltage drops to the pcb, hence you need to compensate by upping the PSU voltage.
Make sure your power and Gnd wiring is of adequate gauge. Some JAMMA harnesses (ones found on eBay) have thick power wires but in most cases they are just thick insulation. Also, some of them only have one or two wires going to the 4 pins of GND and 5V. You should have a single wire attached to each power pin on the JAMMA edge connector.
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