In my opinion '91-'95 XJ's are the best ones to look at. '96 up have OBDII engine systems that will require you to pass emissions testing (plus the OBDII is a bit more picky if you plan to do much engine modding). '87-'90 4.0 used a Renix injection system that's harder to do diagnostics on and the parts are more $$$ due to it being used only on the XJ for four years.
We all know the D35 rear is a turd!!!!!! But that's what was used in the vast majority of XJ's. As Jon pointed out, the D44 was a very limited offering into the late '80s. The Chrysler 8 1/4 started showing up in the early/mid '90s with 27 spline shafts and 29 or 30 (can't remember which) splines in the late '90s. They're stronger diffs and gears than the D35 but the early 27 spline isn't any better than the D35 shafts (at least you'd have a stronger diff!). Also, C8.25 upgrade parts tend to cost more $$ than other axles. If all you can find is the D35, you could pick up a late model 8.25 and bolt it right in, or do the famous 8.8 swap for fairly short $$.
I wouldn't worry too much about intakes at this point! The '99ish up "horseshoe" will give a bit more power in the mid to upper range on an earlier engine, but it's not enough to make a big difference. The best part of doing that swap is converting the power steering pump to one that's MUCH easier to adjust the belt tension on than older models (that in itself was worth it to me!)
The biggest thing to look for is RUST!!!!!!!!!!!! Contrary to what the used car dealer told Eve, newer vehicles DO rust and the XJ is a pro at it!!!!!!!!!!!
Rocker panels are famous for rotting out on 4 door models, so unless you're planning to box the rockers like I did........ The floors also love to go away allowing you to pretend to be Fred Flintstone! (I'll take a pic of my brother's '88 with 217K on the clock to prove it
) Sometimes the uni-body will rot where the gas filler tube passes through, and main eye bolts on the rear springs are known to fuse to the bushing sleeves.
FjR68