Try putting the front driveshaft back in and removing the rear driveshaft and see if it continues. Put it in 4WD when you do so so that you are driving in front wheel drive. If the clunk continues, it's probably related to the transfer case, transmission, or other upstream component.
Inspect the u-joints on the driveshaft while you have it off.
While you have each one off, check the transfer case outputs and the pinion shafts for any play. (A small amount of rotational backlash is normal, but excessive backlash or vertical/lateral play is not.)
Check the motor mounts and transmission mount to make sure they haven't become damaged. If the rubber in the mount looks rotted, it probably needs to be replaced.
Check all the leaf spring mounts and shackles for loose hardware. Loose spring mounts or shackles could make a lot of noise on sudden acceleration or deceleration. Check the transmission crossmember/skid to ensure all hardware is tight.
If you are still stumped after the above, I recommend changing the fluid in the transmission, transfer case, and front/rear differential. If you see any excessive metal shavings in any of those, that could be cause for concern, and may or may not be related. (Regardless, it's a good idea to refresh the fluids in an old vehicle which has an unknown service history.)