For my understanding PWM-Method is canceled and maybe oversized.
The extension port is placed in the middle of the board and you can switch two channels with it.
There are four pins in it, two pins for each channel.
For instance you can switch a shaker an channel A and/or a fog-machine or lightshow an channel B.
Both channel switch 5 volt.
A separate power supply is necessary not only for Indy... all pinball machines can get in trouble if the power supply is being overloaded and then they will reset or burn the connectors/wiring.
I bought my relay and rev limiter at ebay for a good price ~7 Euros each.