Congratulations on your new Wrangler. While I can't tow my '01 without dropping the driveshafts due to the aftermarket transfer case I do flat tow both of our Cherokees, the TJ/XJ series are great toads.
As to your clunk, due to the abuse mine sees I've found a multitude of places that develop acceleration/deceleration clunks. If the sound is from the front first bet is the knuckle U-joints, take a pry bar/screwdrive and lever the inner shaft to check for play. Bad driveshaft U-joints will usually have a vibration associated with them, grabbing each end and giving them a good tug will check for excess play.
Another clunk generator is the control arms, put a wrench on the bolt on both ends of all 8 and check the rubber bushings. If bad, they will clunk as the axle tries to rotate under acceleration and deceleration.
Have fun and enjoy the trails. And remember to check with the local Forest Service/BLM to find trails that are legal. People going where they shouldn't is the major cause of closed roads/trails.
Webmaster/Land Use Officer, Creeper Jeepers Gang
, Durango CO
The above post is just my experience/opinion which is worth exactly what you paid for it.
'05 Lance 845/'06 F-250 or '99 Alpine 36SDS Usually towing an '01 Wrangler locked on 35"s or moderate '98 Cherokee on 33"s (rear locker only)