I don't think this would make a difference to anybody who cares about the existing original vs FPGA qsound implementations. It certainly wouldn't get me to change up my CPS1 multi setup.
Not trying to be mean. But that is an awful lot of issues. I suggest getting more practice with soldering before trying again.
The power LED on the minigun might be connected backwards. That is a common problem people have.
When you say "the microchip" I assume you mean the THS7374 video amplifier. If that is left unpopulated, you obviously won't get any video output from the minigun. Though maybe you can see some LEDs light up and hear some audio out from your jamma board.