Really sounds from all your issues that you are having serious grounding issues. Check them all, check ALL fuses again under the dash and in the engine bay. I'd add a second grounding cable/strap to the passenger's side in addition to replacing the driver's side main strap if you haven't already.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.