In January of 1999 I swapped out the 5.0L in my 87 Mustang GT for a 32v DOHC 4.6L out of a 96 Mustang Cobra. What a task it was, but well worth the agg. Many attempts to gain information regarding this swap were made but nobody could give me definitive answers to the questions I was up against. I made calls to many people, even modular specialist Sean Hyland in Canada after a very brief article I read that he had wrote in an issue of MM/FF about performing this swap. Just to summarize some of the more important aspects from my own experience that I dealt with, the engine fits well if your using a k-member from a 94-present v8 and it bolts right into the fox body. If not used, the cars existing k-member will need to be modified. The T-5 wont work with the 32v 4.6L so your going to either need the T-45 or something along the lines of a tremec. Using the DOHC 4.6L the vacuum brake booster also will not work since its in the way of the massive cylinder head. I plumbed in the Cobra's hydra-boost system with my original master cylinder with some custom modifications done to that as well in order for it to properly operate. And the hardest part of the conversion for me was just getting the engine to fire and stay running. Everyday for 3 months, after the engine was physically in the car, I would have my nose in the 87 and 96 electrical books figuring out which wires needed to go where. I wound up needing the Cobra's steering column for its key, ignition cylinder and PATS module. Also, I took the wiring from under the dash for the OBD-II connector and wired that into my car so I can scan the engine controller and check for codes if I ever encountered a driveability problem. I inquired about Auburns "Speedbrain" computer system to replace the factory's but one was not yet available for the DOHC 4.6L.
As far as durability of the Mustang 4.6L as compared to the Lincoln....I'm not sure but I figured if I was going to go through all this trouble to do the swap, I'll be damned if I'd put in anything less then the balls to the wall 305hp stock Cobra. And just to complicate my life a little more, only 600 miles after the swap I fitted the car with Vortech's S-trim Supercharger. Pictures and description of the car can be seen at the address below. It is also for sale
http://hometown.aol.com/gottij1033/