I just realized you posted again, and that ground is definitely the problem. The 4 or 5 layers of protectant the auto manufacturer puts on the body is really hard to take off. a wire brush just won't cut it. You will need a grinder to get down to the bare metal. But my first suggestion will always be to ground to the frame, lol. It's the safest and best ground and if you can get all grounds to attach to the frame, it will help things run better, give you less noise introduced onto the system and facilitate higher output voltages from your amp and allow the whole system to run more efficiently.
I hope you like your new system, cause it sounds awesome!!!!! If I can help anymore, please let me know!!