Is there a booster swap from another vehicle that works or just aftermarket...what do the guys running giant one ton brakes run?
the '95.5 YJ has the dual diaphragm booster that was on the TJ so that would be one upgrade.
if you have bigger brakes (larger diameter rotors and/or larger pistons in calipers) you can go with bigger diameter master cylinder:
larger rotors means more stopping power - if the caliper diameter is the same i would keep the same master cylinder
larger diameter pistons in the calipers - this means you get better ratio between master cyl and caliper pistons so more stopping power, downside is more travel so in that case a larger diam master might be needed, if your new ratio is better than the old one you get better stopping power
(new_brake_rotor_diam*new_piston_caliper_diam)/new_master_Cyl_diam the result should be bigger than the same calculation for the stock dimensions and you get better braking (keeping the same booster in this example).
i can go into more detail if you want me to.