my 90 sc with a 408w turbo 5spd still sports the stock hood and closes just fine too, although if you tap on it close to the center top it won't flex
you may need a different oil pan as the cougars pan may not fit, i got a canton 7qt and it cleared almost fine, the damn front sump drain plug hit the stock crossmember and cracked it
i had to completely remove it and just fill weld it doing away with the front plug, my engine is lowered right on top the k and pushed back an inch by swapping mounts, but anyway that was a few years ago, these days i think damn near everyone makes a comparable pan for about 8x less than what i paid for mine
i also had to shim the k-member 3/8" using spacers so i could retain the stock hood
i used an edlebrock super victor efi intake and ultra low profile carb to t/b elbow designed for the vettes, i had to cut the top lip off the elbow so it would clear the hood
i got a flywheel and starter for a 95 f250, the "5.0"s have a different imbalance than the 351s, (unless its a "302" from before 81 which it may have the 28.8oz imbalance as the 351, im not sure what your engine is balanced too as im not sure if the 351s ever changed??? My engines came from a 95 and 96 f250 thus i have the roller blocks and those are def 28.8oz
that about covers the mechanics
computer wise, the 91-93 5.0 mn12 94-95 v8 mustang and the 95-96 mass air 5.0 & 5.8 trucks all use the same exact wiring harness, the computers are all interchangeable, the most desireable ecu of those 3 is going to be the sn95 ecu as it has the most programming support
going from a stock supercoupe to a stock 351w isn't very fun, the supercoupe is definitely more exciting, i'd recommend a set of rhs heads and at a minimum retarding the stock cam a few degrees, i couldn't be happier with the super victor intake, its rated from 4500-8500 or so but i got no problem with 3rd gear take offs plenty low end torque
hope this helps