Here's a good website to look at when wondering what happened to the XJ's over the years.
http://www.edmunds.com/insideline/do/Features/articleId=46011
I like the older H.O. models, from 1991-1994, because they're still simple to work on, have a little more oomph, and there's a LOT more out there when it comes to go-faster parts. Suspension didn't change much at all throughout the years; so a lift kit for a 1984 will still fit on a 2001 XJ.
The older models, (1987-1990) have the Renault/Bendix (Renix) engine management system; a little more complicated, but you can diagnose pretty much any sensor with a Multi-meter and a manual. The engine blocks are made of sterner stuff too.
The common consensus about best motor/tranny to get it a 4.0 litre and an automatic transmission. Avoid 1984-1986 models because Jeep was still working out the bugs with the 4-banger, and the 2.8 V6 isn't a very good motor. (It can be swapped to a 3.4 for more power, but is still limited when it comes to upgrades.)
Look for rust issues, especially if you live anywhere that they use salt. Look at the rocker panels, rear quarter panels, the driver's footwell, behind the rear wheelwells, and the bottoms of the doors.
Blow-by is an issue, but not a big one. If you find oil in the air-filter and the engine has great oil pressure; it's probably just a clogged CCV system. Easily fixed!
All 4.0's have a bit of piston slap, don't let it bother you.
The early models (1984-1986) have good transfer cases, but are limited in aftermarket support for them. The later years, (1987 and up) have either the 'Command-Trac' NP 231 (transfer case bezel says 2-hi, 4-hi, N, 4-lo) or the 'Selec-Trac' (transfer case bezel says 2-hi, 4-part time, 4-full time, N, 4-lo). The 231 is easier to work on, slightly cheaper to replace, and has loads of aftermarket goodies (especially Slip-Yoke-Eliminator kits.) The Selec-Trac is an awesome case, but just doesn't have much market for add-ons. (The full-time option is sweet if you live in an area with a lot of snow.)
Going 4-6" will probably give you vibrations from your driveline angles. This can be fixed by lowering your t-case, or adding a SYE. (The SYE is around $200 and up BTW.) If I were you, I'd only lift it 2" or so, and then trim the fenders for extra clearance.
Hmmm... That's all I can think of for now. Anyone else?