Here is documentation I found on the LED flashes.
Most boards in the backbox of a Gottlieb System3 game have a diagnostic LED. If a
system3 game boots correctly, here is what each board's LED does.
A1 CPU Control Board LED.
The CPU board's single LED will flash continually and evenly if the board boots
correctly. If the CPU board's LED flashes very fast for a second, then pauses just a
moment, then repeats, this usually indicates a low CPU board battery or a bad U11
chip.
A8 Dot Matrix Controller Board LED.
The DMD (Dot Matrix Display) Controller board's LED should also flash continually
and evenly (but not quite as fast as the CPU board's LED). If the DMD Controller
board's LED is stuck on, this usually means there is a problem with the custom GAL
(Generic Array Logic) chip at U8. The GAL is a programmale chip that replaces
several 7400 series TTL logic chips. A bad U8 GAL chip will also cause the DMD to
show "garage". This chip is available from a number of sources (but must be
programmed).
A6 Sound Board and A20 Auxiliary Sound Board LEDs.
Each of these two sound board have an LED. Both boards' LED should be flashing
continually when the game is powered on. If neither LED is flashing (off), usually
this means the sound board to CPU board connector at CPU board P4 is
disconnected. Or there is no +12/-12 power coming from the Auxiliary Power
Supply.
A3 Driver Board, A1 Power Supply, A5 Aux Power Supply.
These three boards do not have any LEDs. But if the A1 power supply is not
working, none of the other boards will boot. If the A5 Auxiliary Power Supply is not
working, the two sound board LEDs won't light either.
Sound Board Dual "Screech" Sound at Boot-Up.
One thing common to all System3 games is the bootup two tone "Screech" sound.
If the Auxiliary power supply is working, fuses F10/F11 are good, the speakers are
connected, and the Sound boards boot-up properely, the game will make two quick
and obnoxious high pitched squeels as soon as the power is applied.