purchase a wrecked 1994 or 1995 mustang gt with the transmission you'd like. it will have all the parts you require, and likely be the lowest headache/lowest cost method.
motor
trans
engine wiring harness
fuse box and front accessory wiring
dash, gauge cluster, dash wiring
ECU
K member and motor mounts
driveshaft
headers, midpipe, intake tube
fuel tank, pump, sender, lines
steering rack, power steering lines, brake booster, brake master cylinder, misc brake lines
A quick list off the top of my head.
The closer you come to making it an OEM 1994 or 1995 GT the easier it is going to be to upgrade the car in the future, fix possible issues, diagnose problems - if you start cutting and splicing and "making" stuff work, congratulations you own a completely custom car, I hope you know how to fix it.
This is one case where I believe in this economy I think it is cheaper to swap yours. 1994 and 1995 GTs in working condition are skyrocketing fast, where as your NPI is falling fast. You would need to find a wrecked one or a very heavy "rebuildable" in order to make it cost effective, something no buyers are looking at to put back on the road. Just "easy" wise it makes sense to outright buy a working 94-95GT and sell your car, but it depends on the deal you find on the wreck and your mechanical ability.
As far as the comments about customization/time involved, if you get a complete donor car there is zero customization involved, it is straightforward parts replacement. As far as time involved, a normal person could take a week off of work or school and bang this out in 4-5 eight hour days. If I still worked at the dealer and had access to my three lifts side by side and a lot of exclusive tools (like a trans jack, overhead engine dolly, etc.), this could be done in a day or two working hard.
