I am build a 2 player cab. Each player has 6 buttons 1 joystick and 1 start button.
Thats 6 total plugging into jammaplus and 14 regular jamma connections total. There are a bunch of wires plugged into the jamma harness that go nowhere (just hanging there. I noticed the player 2 start button is not attached to anything at all.
Q1.Should I plug it into the jamma plus screw terminals on the jpac and program it in?
Yes, this is what I would do. But before you do so, verify that the cab's wire harness is wired correctly and that all the wires you need are connected to where they are supposed to go. I never trust what some conversion-hack-tech did to a cabinet, I always go through all the wiring to make sure it is correct before I plug anything else into it. It's not worth risking frying a J-PAC just to find out later that the cab wiring was messed up.
Q2. Where should the coin door wires be going to and how many are there. There are a bunch of wires on the coin door and a bunch go to a weird connector.
Many coindoors also had vibration switches, coin counters, and lamps that may be connected to the harness. Again, what I do is pull out any wires that I'm not going to use (coin counter, vibration switch, etc), and just use what I need, which is typically just the coin detect switch and the lamps (if you have them). Depending on the coin door, your lamps may take either 5 or 12 VDC. Some cabs used other AC voltages such as 6.3 VAC for the lamps, but those can be connected to a 5VDC source instead.