Roush which way should I go with my engine mods?

I am looking to get some big HP from my 02 S281 N/A. I know to do that I will have to have the engine ripped apart and rebuilt from the ground up and then get a super charger. Would it be cheaper having somebody do that or would it be cheaper to purchase a 03/04 SVT Cobra engine and have then installed into my car. I was checking ebay and right now there is some guy that has two complete cobra motors from 03/04 and once at 6K and the other at 8K since it has 500 miles on it. He says they come with everything you need (computer, etc...) to install except the 6 speed tranny. Will that cobra engine bolt up to my 3650 5 spd? or do you have to swap that to a t 56? Thanks.

Cool thanks for the tips. I just thought that the cobra motor was gods gift to mustangs since everybody brags about them so much. I guess i didnt check into it enough to realize that a 2v can be built up to a pretty sweet setup.