The T-5 is a lot stronger than it gets credit for, actually. A lot of people run them deep into the 12's for extended time frames. The T-5 was never designed to take even a mildly modified Mustang 5.0.
As far as the 93 Cobra, it dyno's closer to 220rwhp stock. They made about 260 at the crank.
Saleen GTS put a full bassani exhuast (long tubes, X pipe, catback) onto his '93 Cobra and dynoed 265rwhp. That's about 320hp at the crank.
The 1993 Cobra is no 235hp engine.
Cobra Intake (200cfm)
GT40 Heads (185cfm)
1.7:1 Roller rockers
Cobra Crank underdrive pulley
24lb/hr injectors
65mm T/B
70mm MAF.
It's basically a receipe for a 320hp Ford 5.0 crate engine. Just detuned all to hell. Gears, exhaust, MAF, A9L will put that car well into the 12's. You're talking $800 in mods to drop it into the 12's without pulling a valve cover. I could do those mods in a single day.
The GT had
HO intake (136cfm)
E7TE heads (155cfm)
1.6:1 stamped rockers
Standard pullies
19lb/hr injectors
60mm T/B
55mm MAF
Do the comparison, if you really think the Cobra would only make 10hp more than the GT you can keep dreamin'
As for the new tranny being more efficient than a C4, I'd be highly skeptical of that. Electronic controls don't really do much for efficiency. The valve body, line pressure, turning mass, and torque converter determine that. The C4 is very light, has a quick and responsive valve body, and it has a relatively small converter.