It would be more trouble than its worth, the entire harness would have to be changed along with the computer dash Assembly and so on .................... if you want a mod car it would be better to try to buy one, you would have a ass load of money in a swap like that anyway so put it on a 96 or newer Cobra.
Swap should be fairly easy. You can buy a 01 Cobra motor from Ford for around $6k and it includes the motor, tranny, engine wiring harness and computer. Everything you need right there in one package.
You will need to change to a 96-04 mod motor k-member though. They are different than the 5.0l k-member used in the 94-95's. With all the people who have changed to tubular K's you shoudl be able to pick one of these up fairly cheap.
So take a high mileage 94-95 v6 with a good body for a few thousand dollars. Buy the 01 Cobra motor package from Ford and swap out k-members and rear ends. Then upgrade suspension and brakes. For a little over $10k you have a Cobra clone with a brand new motor and tranny. Not too bad in my opinion.