I have an 04 and can give you some pointers.
It is the last year for the SFA in the WJ.
Get the V8, no questions asked. The 4.0 is a dog in the heavy WJ. Get a 4X4 with the factory tow package for the power steering and trans coolers. Do not get the 4.7 HO motor in the Overland or Limited. You have to run premium octane with them, $$$$! I personally like the Special Edition models the best. They are a middle model between the Limited and Laredo. You get the nice body color cladding and not the gray stuff on the Laredo. They were only built in 02 and 04 also. The SE's have all the same creature comforts as the Limited but come in a hair over the price of the Laredo.
Stay far away from the dual climate controlled interiors in any model. They have a bad problem with blend door failures and you pretty much have to pull the whole dash out to replace them, not fun at all!
WJ's have a history of warping rotors fast. There is a one time only recall on them. Once they are done at the dealer you are on your own after that to fix them. The best fix is to get Stillen or Powerslot rotors when they do warp. Also making sure the tire monkies torque your lugs properly will help some too.
The heated seats can be funky as well. They can stop working at any given time or just stay on and boil your boys.
The window regulators can and will brake at some point. Pretty much the same problem as the 97+ XJs have.
The reason I suggest the SE is because they normally do not have heated seats, daul climate control, or the HO motor.
PS: If you plan to lift it do NOT use a Rustys lift, go BDS or nothing.
Good luck and I hope this helps.
Here is my 04 SE