On stock heads, TB, EGR with a stock cam, the Cobra may make a couple more HP than a properly ported lower on a stock upper, but the Cobra is the better intake - it just costs a lot more. Also, it can grow to flow up to 250cfm and the stock intake is done at an economical outlay in the 180-190cfm range. The Cobra stock flows 205-210cfm. The heads will determine what intake is most suitable. I've had a BUNCH of customers that don't go beyond E7 heads (stock or ported) or GT40, GT40P heads which a ported stock intake work very well on and produce a very healthy torque curve.
I just dynoed today with my new combo. I hit right at the HP I thought (257HP SAE) but my torque curve is extremely good. I averaged 284RWTQ across the whole 2,000-5,600 rpm power band. I care more about torque than HP for a street car and if you have experienced 275ft-lbs at 2,000 rpm you know what I mean. I was ALL smiles.