Do you have a SYE? If so, grease the slip shaft on the rear drive shaft.. might as well do the front too. If not, grease the slip yoke on the transfer case. 90% sure that is your sound. Mine did it on a complete stop as well when you accelerate away from a stop.
see if you can put it in reverse with your foot on the brake, then pop off the brake and hit it again. if it thuds and you can make it do that over and over before it starts to move check your trans mount. if the rubber tears it lets the trans move up and down.
I'M going to tighten the bolts on my xj at the 500 km mark just as the 3" lift instructions state should be about a week or so longer, at this point i'll go with some of your suggestions and post what worked, thanks for all your help so far
I would retighten everything, then rock the thing back and forth real hard from outside while parked and see if you can replicate the sound. Maybe jack it up and down to simulate weight transfer.
I know this sounds dumb but I had the same problem only it was after putting my lift on. Turned out to be my ratchet and extension in my tool box flopping around. I felt pretty silly after figuring that out.