The Mustang Cobra was detuned to avoid warranty claims on the T-5. While it did have a Cobra intake and GT-40 Iron heads, in addition to a 65mm T/B, and 70mm MAF, it also had a less aggressive Cobra specific camshaft, and a computer that used very conservative fuel/timing curves. Anyway, just a couple quick changes and those '93 Cobra's pick up a whole lotta attitude.
I wouldn't bet on a '93 GT outrunning a '93 Z28. With equal drivers, stock for stock off the floor, I'd expect the '93 Z28 to pull nearly 1/2sec on the '93 GT in the 1/4. That being said, given a few years, the LT-1 is tired and broken down
With the aforementioned changes to the engines, I don't believe the MAF cars made as much hp as the SD cars from the factory. Most of the 1/4 mile times I see seem to indicate that as well. The fuel/timing curves in the computers likely got a little less aggressive as time went on, but that's just my theory.
Technically, I would think that the hypereutic aluminum pistons in the '93 would make more power than the forged pistons. Not only was the seal better (less oil consumption for emissions) but they should be lighter.