it is possible to do so
i thought of the idea of taking my 5.4 l motor and putting it is my t-bird sc. but it is so much work and changes the waight distrubution on the car.
for you i think it might be alot better just to use the cobra drivetrain/parts on the 4.6L as it seems that alot of the cobra guys are putting down even better #'s make sure to get those forged rods and cobra internals if you add a sc.