You must have one of the more recent Factory 5 Racing Cobra kits, since only the recent kits support mounting the modern 4.6L Ford engines. And you would like to use a 4-valve motor from an SVT Cobra or Mach 1 model because of the higher HP output.
If you can get a 4-valve donor car, you should use the factory computer from it with the engine and
trans.
If you can't get a 4-valve donor car and decide to buy a crate motor, why don't you get a carburated motor and make the Cobra look more period correct? They sell wiring harnesses for that, and you don't have to worry about any computer.