Were both of your XJs 4wd?
The best my MJ has done is right around 20 mpg. It has only done that on one tank, every other time has been in the 16-18 range for highway driving, so I think you're right in line with what you should be getting.
I think there could be a number of factors for the worse fuel economy. Needing a tune up, like you thought, the lift is a big one, and MJs are naturally a little higher than XJs it seems and probably less aerodynamic too. From my experience, 4.0s actually like some RPM, so the factory 3.07 gears are hurting you some. 3.55s would probably yield better mileage. It is also worth nothing that the cylinder head, intake manifold, and exhaust manifold (possibly the cam too, I don't remember) changed in 1991 when the HO Jeeps came out. All of those let the air flow better, which will help gas mileage.