I used an '01 XJ booster. I Used a 1/4" spacer between the firewall and the booster, but the brake pedal was still 1" higher than stock. I didn't want to pull the MC out, so I pulled the brake pedal, and welded a "nub" on the back side , drilled a new hole for the pedal, and all is well. The new hole is 1/4" lower, and 3/4" behind the old hole (actually 1 1/16 back from the front edge of the pedal.
The '88 XJ booster rod was 4&15/16, while the '01 rod was 5&15/16. Because of the angle at which the '01 booster sets to the firewall, the new hole will be lower on the XJ pedal (1/4").
If I had known all of this before I did the swap, I would have cut off the end of my old booster rod and would have sleeved and pinned it to the new booster rod, after shortening it--I wouldn't weld on the new rod, for fear of "melting" the booster's internal seals/gaskets.