I put a WJ booster and master in my 92 MJ. No mods were needed, but it's probably different for an 89. I also have Explorer rear discs, ZJ prop valve, and I got rid of the load sensing valve.
Yes and no. The 96 MC rod has to be modded slightly so that the brake light switch works properly. I used a round file to open the hole up and then a grinder to put a flat spot on the end of the rod. The only other mod is just hooking up the brake lines.