You already have a decent MAF, air filter, intake, throttle body, heads, RR's as well as some other goodies. Don't butcher the Cobra.
If you want better shifting and such get:
A better shifter: Steeda Tri-ax and Pro-50 are probally the best. Others are good but it seems most are happiest with those two.
Quadrant/Cable kits: Most overlooked, the stock linkage sucks, esp. when it gets some wear and age, causes a lot of issues.
Otherwise:
Subframes would stiffen the chassis a great bit and help restore the integrity of the car.
Determine the gear, 3.55's are decent, but any lower I would get a 3.73 or if your feeling really hairy, 4.10's. Traction-loc rebuild is recomended at this time.
The stock cam is a real setback for the 93 Cobra, it is actually worse than a stock HO cam. A custom cam or even a better mild cam would make a decent difference.
Those heads outflow stock, but can really flow a lot better with some porting. If you do this, maby the intake would be good to port at that time, but wouldn't be a bottleneck if you didn't.
O/R mid pipe and exaust, maby headers. Your motor just can't breathe that good through 4 converters.