My 94 XJ has a Exploder 8.8 rear, 95-96 booster upgrade (which I wholeheartedly recommend as easier than WJ), ZJ valve internals and the same pads all around. The rear locks up ever so slightly before the front, which is exactly how I like it.
Installing a larger diameter master cylinder alone NEVER increases braking performance. Sure, it improves peddle feel, but pressure at the pads is reduced. Too small a MC makes the brakes "touchy". Nothing, nothing, nothing, face plant into steering wheel... All because the smaller diameter piston generates a higher pressure from the input force from the vacuum booster and your leg. Think grease gun vs bicycle tire pump...
That's not to say that there aren't times when a larger MC is warranted, particularly when you install calipers with more piston surface area. The area ratio is restored, pedal feel is improved and they're no longer "touchy", but do understand that you reduced pressure at the pads in doing so. As you continue to increase MC piston area, you eventually end up with the same low pad pressure you get with a single-diaphragm booster and stock brakes. The ONLY way to improve braking performance once a larger MC is warranted for "feel" reasons is to install a larger diameter dual-diaphragm (do they make triple diaphragm?) or convert to hydro-boost. It's all about ratios. Keep all ratios roughly the same and all is well. Check out the booster on that 3/4 ton truck. It's 11" diameter (190 sq in) vs 8" (100 sq in) for the WJ, almost double...
Braking performance isn't solely about pressure. Haven't done it myself but I hear you can do a WJ swap, install a slightly larger MC to get a better pedal feel and still have improved braking over stock do to increased pad sweep area, but do understand that actual performance at the tires is reduced compared to the smaller MC. WJs, XJs, all the same 1" diameter MC but one has small calipers and drums, the other big calipers and discs in the rear.
Back to the 95-96 booster swap. Completely bolt in other than the brake lines to the prop valve and a 1/4" spacer at the firewall. Done. Not nearly as many of them in JY so it's not as popular, but the diameter is same so the same performance. Other than regular maintenance items, before making any changes to your braking system, if you do not have a 95 or newer XJ, or have done the 95-96 XJ or WJ booster swap, you MUST do it. You're almost doubling pressure at the pads by doing so...