Well since the I-Pac has 2 ground ports coming out of it, if you connect one of them to one side, and the other to the other side, you're golden. Here's to answer you're questions:
A) it doesn't matter where you start with the ground, as long as it's a full loop around the P1 or P2 side. The best I'd say would be to start on the P1 right, do a circle around the joystick, then go to the buttons, and finish off with the 1 Player start button, and connect your first ground to that Player 1 start button. And vice versa with the Player 2 side. (If you really need help, I'm going to have a drawing of my grounds that i need for when I take off the prototype on my control panel, and I can scan it for you.)
B) I would say get some kind of non-conductive foam (I used those bubble things that you can pop) or something and place it on the bottom of the I-pac, then just find some small screws that will hold the I-pac in place, and maybe some tape just to be safe.
C)Yeah, sometimes the Supers will do that if they're mounted a certain way, I don't really get why they do that sometimes, but I know what's causing the sounds. It's because the black actuator on the bottom of the joystick shaft is actually slipping over the microswitch levers, and it makes that loud TWANG noise. I heard this one guy put a plastic O spacer on the bottom of his shaft, so it prevented the Actuator from going over the levers. I'm sure you could rig something like that up in 2 seconds, so just experiment with it.
-Good Luck
-CthulhuLuke