Good luck getting it to fit into a Cobra! In Muscle Mustangs & Fast Fords magazine, they put one in a Fox body Mustang. It required a 6" cowl hood to fit the supercharger under the hood.
I didn't see an '03 Cobra engine on Mustang Parts Specialties website, but they have an '00 engine listed for $6000. So I'm guessing $8000 for the '03 engine. Add $1200 for bolt on, and you're up to $9200. For that money you could build a 427 SO or a heck of a stroked Windsor that would blow the '03 Cobra engine out of the water. (I've got $6000 into my 500hp 408W).
BTW, Mustang Parts Specialties prices are awfully high - you can get much better deals elsewhere.
EDIT: I just noticed they don't accept credit cards for engine purchases, just direct wire transfers. Wonder why that is???
Pete