It is hard to tell the difference in a well running 5.2 vs 5.9, in the real world they are very close in power unless one is real sacked out. I worked at a dodge dealer when they were new and I would always try to guess witch one was under the hood before looking and you couldn't really tell. The 5.2 had a flat top piston that would promote better combustion flame travel, more compression and a better cam (shorter duration higher lift).
The 5.2 often came with a 44RE instead of the 46RE that gave it a better 1st gear and 2nd gear ratios and less drag from the heavy parts and for some reason the smaller trans doesn't seem plauged by the same problems the 46RE had.
If I had 2 identicle rigs to pick from except the drivetrain I would pick a 5.2/44RE combo over a 5.9/46RE combo. It is just as quick (maybe quicker) and better on fuel.
The one biggie now that throws it all out the window is how well the rig has been cared for over the last nearly 20 years. I am not talking miles as that is a bogus way to judge a vehicles worth but how it was driven and maintained. Some people completly trash a vehicle in 50,000 miles while others will take good care of the same kind of car and have a car that rides, dirves, works like new with 300,000.
1998-2000 are pretty much the same rig, 2001 they got a little different interior, little easier to work on things like heater core and air doors but a little more likely to have issues than the older ones, pick your poison. Avoid the dual zone HVAC (became an option in 2001) if they are otherwise equal rigs but again there are bigger things to worry about in the big picture.
00 or 01 the 4x4 went from a steering gear box to a rack and pinion. I never seen much trouble from either but the R&P steers maybe a tiny bit better but think big picture.
The rear HVAC can be a pain, big long lines run to the back that like to leak as well as more moving parts that break ocasionally in the rear unit.
2003 and maybe 2002 got rear discs but the rear drums never bothered me.
Around 01 it seems they did away with the 15 inch wheels and went to 16" but they all seem interchangable, the R/T was full time 4wd and got 17" wheels and 3.92 gears and limited slip rear diff. I would try to avoid the 3.92 gears (most came with 3.55s) unless you just need a little more gidyup as it does take small MPG hit. I have seen a couple non R/T with full time 4wd, I would avoid it personally as it is another MPG hit that is not needed and you can feel the extra drag from it, the one we converted was a lot less heavy feeling after the swap to 2wd option.
