Sorry to be tardy to the party. I'm on vacation in Outer Banks, NC.
Edouard is correct on the history of powerplants in the Shelby Cobras. The originals with the 260 and 289 engines were what they called "slab side" bodies. Very flat on the sides and minimal fender flares. When they added the 427 FE side-oiler, the body took on its more familiar muscular shape with the generous fender flares and the vents in the front fenders.
These days, there is a wide variety of engines that are offered in the replicas. While some still sell the 427 big-block side-oilers, many choose small blocks. Everything from original 289 to 427 CID from the Ford Windsor small block.
I'm not sure, but I think that most if not all of the aluminum bodies now being sold are made by Kirkham Motorsports in Utah.
http://www.kirkhammotorsports.com/ And I think their bodies are hand made by craftsmen in Poland. I haven't looked into them in several years, but if I was in the market for a new Cobra Replica, Kirkham would be my first choice.
Mine is a fiberglas body, unfaithful replica. I call it a street rod that looks like a Cobra. Bigger flares on the rear fenders, totally different interior, one-piece double roll bar and 521 CID V8 (stroked 460). I would do it differently if I were to redo it, but I've moved on to Buicks now!
Pictures attached. Take a look and think of how many people comment on the car. Most think it's a Mustang....
Chuck