So I just ran across this thread, and I love it. This was our goal with the 94' Cobra, and if you are interested, I'll post as much build data as I can. We wanted to build the Cobra car that Ford should have built in the first place. We went as far as to find the original stickers for the valve covers, put them back on, and even ordered an OEM distributor condom. We managed 302hp to the wheels. A couple things that weren't stock, we used Ford GT40x aluminum heads. You really can't tell it has aluminum heads on it, but if you wanted to call the way, their are coatings that make them look like iron ones. We also used long tube headers, but I think you could find a set of short tubes that wouldn't be far off stock. I managed to cram a giant 78MM PMAS flow meter into the stock air filter box. The engine itself has GT40x heads, the short block is rebuilt and zero decked to get 9.8:1 compression ratio. It has an off the shelf Comp Cam in it, but tuned correctly it does idle pretty close to stock. The stock Cobra intake was ported by TMOSS. You will go no where with a stock GT intake. However, if you get a Ford Explorer intake and have it ported by TMOSS, it will flow 250cfm, and you'd have to look real close to tell it's not a GT intake. Or you could put a Cobra intake on it, and with the right display plate, it would be hard to tell as well.
Kurt