Ok, as a Grand guy I will let you know whats up.
There are 2 big issues with WJs. The Limited models have AC problems with the blend doors. Lots of work to fix it, see if it has been done before. The other thing is that the early models (99-01?) have problems with warped rotors. Again, see if that has been fixed. Both of those were recalls so they should be fixed.
Now, I have never heard about any trans problems really. The V8s have 5 speeds and the 6 cylinders have 4 speeds, both autos. One neat thing is that the early V8 trans are only 4 speeds but can reflashed to gain that 5th gear. The V8s are very good motors. 4.7L, 235 hp, 295 lb.-ft. (I think, going off memory here), so its got good power. The 6 cylinder is your basic 4.0L HO. On the later models, you could get the 4.7L HO with has more power and a great choice.
For the rest of the drivetrain, D30 front and either a non c-clip D35 (I6) or D44a (V8) rear. Both are wider axles then other Jeeps so parts cannot be swapped between them. Transfer cases are either the 242 (part time) or 247 (full time). You can also get a Quadradrive which has the 247 with limited slips front and rear.
As far as an aftermarket goes, for the basic bolt on stuff, its not that bad of a selection or prices. But the more you start doing to it, the more expensive it gets and the harder it is to find parts.
Now, in my opinion, for a DD to mild wheeler, it is a great choice. If it were me, I would find one with the 4.7HO and Quadradrive, lift it 3"-4" and fit 32" tires with basic armor and parts.
And that picture is of a ZJ. I mean really, how hard is it to remember this stuff. If someone called one of ya'lls TJ a YJ or your CJ a Wrangler, would it not piss you off?