I had the exact same problem. The clunking can be attributed to the Ujoints, rear dif(slop/backlash), X-fer case or any combination of the three. In mine it is the rear diff, common, can get by for a while with some tlc but needs to be addressed in the near term. Check all if you haven't done so already.
As far as the hesitation goes, for me it was a rear drum problem. Are you using thr e-brake regularly? if not, it can get stuck and require adjustment/lube. In mine the rear  

S grease seal failed and filled the drum with grease. Changed out both sides, cleaned, ok for a while. Then started getting the same symptoms you describe, hesitation from P and clunk and jolt. Pulled off both drums and measured for serviceability. Both sides were just outside of max diameter(297mm/11.7"?) completely disassembled,cleaned and rebuilt both sides(new drums, pads, springs,wheel cylinders,etc..OEM), lubed adjusters, adjusted all and flushed with new brake fluid and no more problem.
I would post a step by step, but the FSM has it covered.
If you need additional tips,tricks send a PM. all in all a

and 12x

job. HTH