Well, I had a ton of links and info on that swap (4V into a 96-98) but Iv'e lost it all. It's one of the easier swaps with a 96-98 cobra or mark viii 4 valve so i would have to assume the Mach 1 swap wouldn't be too bad, particularly so if you backwards-convert the engine to coil packs instead of coil on plug. I guess the guys that swap 4 valves in extend a few connectors, have the car tuned and are good to go. I guess it depends on how you want to execute the swap.
ModularFords is a great source for swap info.
My swap was a little more plug and play because everything was for a 99-04 car. Very easy swap.
If you want too keep coil on plug and the Mach 1 electronics your going to need pretty much everything. Your T45 will work but i would upgrade the clutch to an 03-04 cobra setup along with the aluminum flywheel. If the engine didn't come with a flywheel you will need one of those to. If the engine was out of an auto you can use a GT flywheel, if it was from a manual car you need a cobra/mach flywheel.
If your car doesn't have hydroboost brakes you can probably count on swapping in hydroboost.