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 build #48. Bolt ons, suspension, Novi 2000.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.