I actually have completed the project you are asking about. I can give you some advice about what not to do.. but in a nutshell - it is a LOT of work. Not to say that once it is all done it isn't worth it, but get ready to drop some cash.
I stripped the car to the bone:
= New 2001 4.6 Cobra motor (Ford racing)
= Manley forged pistons/rods
= CNC head porting
= Kenne Bell charger (15lbs boost)
= FR Aluminum Radiator
= Shorty headers
= X pipe
= Remote oil mount
= Alternator relocation bracket
= 60lb fuel injectors
= Looped fuel return
= FAST XFI electronics
= new 9 inch rear (posi)
= billet trailing arms
= rear suspension
= aluminum drive shaft
= T-56 transmission
= Hurst short throw
= K-member
= Performance front suspension
= Wilwood brakes (the big boys)
= much, much, much more…
The things that are a “pain in the arse” are endless. The 05 computer will not run the motor and adding the stock cobra engine computer to the car is not a good answer. After several weeks of “harness madness” we sent the (cobra) harness to Sean Hyland to modify (it was a joke) got back a useless p.o.s. In fact every single thing ordered from Sean Hyland was a TOTAL piece of crap or was the wrong part. I would stay away from him at all costs. His business is the absolute WORST I have ever dealt with. We ended up using the FAST XFI, their customer support was stellar. The system works great and can handle just about anything and is totally configurable by computer. Easy to learn and operate. Kudos to FAST. Anyway there are a lot of challenges –throttle control on the 05 is “by wire” and the 4.6 Cobra throttle is cable.. so there is modification and adding a new gas pedal, also transmission brackets and relocating a lot of things – there is a lot more but I think you get the picture. The project (in spare time) took a bit less than 2 years. I am very proud of the car – it is truly one of a kind and will eat Shelby SVT’s, Vetts and Vipers for lunch all day long. I haven’t got it to the track yet due to some final tweaking and tuning but I hit 60 in first gear in a little over 3 seconds. I have about $85,000.00 in it now and expect to reach 100K + before it is (totally) complete.
Depending on how much time and effort you want to put into it (not to mention money) you might consider getting a GT instead and just working over the engine. It is not a few week processes unless you have the ultimate shop and team working full time, without budget constraints.
Here are some pics:
http://192.168.1.22/mustang/pic6.JPG http://192.168.1.22/mustang/pic5.JPG http://192.168.1.22/mustang/pic4.JPG http://192.168.1.22/mustang/pic27.JPG http://192.168.1.22/mustang/pic26.JPG http://192.168.1.22/mustang/pic25.JPG http://192.168.1.22/mustang/pic24.jpg http://192.168.1.22/mustang/pic22.jpg http://192.168.1.22/mustang/pic21.jpg http://192.168.1.22/mustang/pic19.jpg http://192.168.1.22/mustang/pic17.jpg http://192.168.1.22/mustang/pic16.jpg http://192.168.1.22/mustang/pic12.JPG http://192.168.1.22/mustang/pic11.JPG http://192.168.1.22/mustang/pic1.JPG
I hope that gives you some insight. I will be glad to answer any questions you may have.
Mark
2003 Cobra motor swap into 2005 V6 coupe HELP 
