You can do it, ive looked into the research on this alot. It will be much harder than just a 4.6 to 4.6 swap. If i could find a wrecked Mark for under 800 bucks i'd buy it right now.
Heres the deal though, dont do it unless your going to build that engine first. Some guys talk about doing it just because their engine blew... thats the wrong idea. The internals are notoriously brittle, and your only going to gain a few HP over just going PI. But if your going to build the engine a bit before hand, or super charge it those heads are supposed to flow even better than the Cobra ones on F/I. And the block is supposedly one of the best ford made. If youve got the money to Port/Polish the intake side, drop some cash on headers and a S/C, and maybe do the internals it would be a great long term project. but just for a one to one swap its going to be a big headache and could potentially be costly.
That being said, heres what you need: to extend or split a few ignition cables, no big there, you will need a new bell housing maybe... since Marks are only automatics. Theres also some valves you have to delete, EGR i think? dont quote me. You will have to buy a cobra intake. Theres also another issue with the ignition that i cant remember, the mechanic i was consulting told me i may want to switch to coil packs and that would be much easier than dealing with the rest of it. Look it up on other forums especially Mark VIII derived ones like Lincoln Vs. Cadillac. Thats where i found alot of the info.
Other than those extremely vague hints that im sure didnt help much. It IS very possible and other than the above already noted problems its pretty much straight forward swap and drop. Ive even seen one in a Fox. ... It should run as you drop it in with your computer... or atleast start. Im sure it would not be optimum but its going to need a tune anyway, but a tune should fix the problem..... you wont need a wiring harness or a computer......
I was looking at putting one in my 04 GT and those were some of the problems, if your dropping it into an SN-95 you will have even less. Do a search for a write up on how to put a cobra engine into a GT to get a baseline. i used to have it but have since lost it. If i find it i will be sure to post it up on here.
Good luck man.
And hey if you dont want that Mark let me know if its real cheap!