I agree, if you didn't have the resources of the internet and sites such as this with people who have been there, done that, then yes, it would be a large undertaking to say the least.
But having been there and knowing exactly what to buy and what will work from the existing setup, I can tell you it's not that expensive, not nearly as costly as finding a "descent" 94/95 GT in good shape.
It's no secret that these cars seem to be ragged out more than any other Mustang, not sure why but in my own experiences it's true. I bought my car all beat up with various body panels of different colors, and I paid 1600.00 for it. It was the cheapest running, driving 5.0 I've seen for sale. And even then I had to replace all the tires and give it a couple hundred bucks in general TLC items. So I still had about 2 grand in the car after all was said and done, and it still looked like crap!
You say you have a nice candidate in good shape, so I think it would be cost effective if you can find either a cheap donor car or a complete swap kit to use.
You can use either the AODE or T5 from the V6, so you can spare that expense.