Do a good brake job on your car and it can make a big difference. Get some better stopping pads like Hawk.
The two piston caliper lets it apply more pressure with less brake pedal effort.
But probably the biggest reason the cobra brakes work better is because of the larger rotors. IIRC the back rotors are slightly larger, but most stopping power comes from the front anyway. The front rotors are a large 13", so the caliper sits further away from the wheel.
Its like using a 16" breaker bar to break loost a bolt versus a 7" socket wrench. The breaker bar is much more capable because the pressure is being applied further away from the pivot point. Same concept with the larger rotors. You dont need crossdrilled/vented anything unless you do a lot of road racing. For street driving, just a plain factory rotor would be fine, and if anything, would stop better(thanks to more pad surface contact area).
And FWIW-I did the front cobra conversion on my old 98 GT with a new kit from FRPP. It worked ok. It wasnt mind blowing, but it stopped a lot better than it did. I just installed new rotors/pads, and bled the whole system on my 02-and that made a nice difference. As it sits now, it stops good enough for me(and Im just using the cheapo pads from Oreilly-brake best I think)