You need to start removing variables.
Unplug the coin door. Power it on. Unplug the PCB, power it on. You need to isolate the short.
So far it only blows the fuses when you connect the PCB- disconnect it and power it on and everything else functions, plug PCB back in and BOOM!! There must be something wrong with this new molex connector, but I just don't understand what. I used the multimeter and it is getting the correct amount of power to the right places... something must be touching somewhere and I am just not finding it