Now that I'm back on a PC, I can expand a little bit.
Lets start up front.
94-98 GT/v6 use a single piston 66mm caliper and 10.9 rotors.
99-04 GT-V6 use the same 10.9" rotors, but with dual piston 44.5mm aluminum calipers. Direct bolt onto the 94-98 cars except the 94-95 guys may need to clearance the spindle slightly for the larger pistons. Not a big deal.
If you want a bigger rotor, the Cobra 13" kit is the way to go. Larger rotors and a caliper unique to that setup. There's a 94-98 version that came on the cobra only, and a 99-04 version that came on the cobra, mach 1 and bullitt only.
Whichever of the above calipers you select, will require a MC change to compensate.
Out back...
all 94-04 use the same calipers, but the cobra/mach1/bullitt use a different pad support bracket to clear the wider rotor. You will need to find these, and I believe rockauto.com and parts stores do sell them separately.
These pics show the part I'm talking about
But as far as the actual rear caliper that pushes the pads...same part on all 94-04. Pads are thinner on the cobra though.
Other than that, for your V6, if you bought the M-2300-M kit for out back. the only part you need to get would be the bracket I showed above. You could then resell all your v6 stuff (same as GT) on CL or ebay and recoop some funds.
Your booster can stay
My recommendations for MC when changing from the 94-98 GT/V6 stuff
99-04 GT/V6 calipers = 1993 Cobra 1" MC
94-98 Cobra calipers = 94-95 Cobra 15/16" MC
99-04 cobra calipers = 1993 Cobra 1" MC