95 Cobra cooling fan

If you jump power and ground directly to the fan does it run?

Coolant Temperature Switch will only give the computer or controller a temperature reading, it is not an on/off thing. Jumping it likely doesn't do anything.

Since the fan works when you jump the two wires at the fan, I would reconnect the fan plug and work my way back up the system and keep jumping the power wire (or signal) as you go.

Which coolant temp switch did you replace? I know on the Foxes (and I believe 94/95 as well) there are two. One operates the instrument cluster gauge, the other provides input to the engine computer (which controls the fans). On a Fox 5.0, the cluster sensor is driver front corner of intake. The sensor for the computer is in the bypass tube running along the passenger side of intake.

Looking at the wiring diagram at: http://www.veryuseful.com/mustang/tech/engine/images/Mustang-94-95-CCRM-AC-Diagram.gif

It looks like the power feed for the fans comes directly from the CCRM. I would unplug that connector and locate the wires to the fans and jump them there to see if the wiring is still good between CCRM and fans. Also check the ground wire for the fans themselves (trace the black wire from the fan connector to where it attaches to chassis).

Try that and let us know.