I’m on a phone so I have to shorten what I really want to type. I’ll revisit when back in a PC.
One drawback to vscuum brakes is inconsistent levels of vacuum leading to inconsistent pedal feel. I can’t drive the car and tell you for sure this is the case but it’s highly likely that is what you are experiencing.
It’s entirely possible your existing booster doesn’t have enough assist what what is a pretty large MC and caliper combo. Barring any mechanical issues (booster rod not adjusted) or vacuum leaks or air in the system, I would start with changing to the 93 cobra style booster.
If for some reason you do not want to swap the booster, I would go down to the 1” bore 1993 cobra MC if you have the standard sn95 38mm calipers. The reduction by 1/16” will soften the pedal slightly, and increase pedal stroke a tad since you aren’t moving as much fluid per linear unit of distance travelled. 93 cobra MC is a direct swap with 94-95 GT. No need to change MC lines.
You really have two options there, but I can’t tell you which to do. Pedal feel is a highly subjective thing. Some folks like firm brakes, and some folks like that modern over-assisted feel.