After all that and you never specified if it was a Duratec (V6) or Zetec(4cyl) engine.
This is kind of important to help you.

If you've rechecked everything you've done and it's a V6 Duratec.
Check the Idle Air Control Valve, Injectors maybe leaking or plugged, maybe do a fuel pressure test.
I could very well just be the old gas and additives you threw in there.

1996 2.5LT V6 Contour ATX My Tour+help/info pics E0 rims, Gutted Pre-Cats,CTA Custom Exhaust & Intake, Diablo Chip.