Depending on the height of your lift kit and the manufacturer it could have added change of axle angle. There are bolt in shims to ajust the angle of the axle to relieve the stress on the drive line. They could have been left in and need to be removed to match the stock driveline,front and rear axles.The binding of the drive shaft u-joints could be the source of the clunk or the shaft is being jammed into the transmission.You might be able to see the shims near the axle ubolts.
If not that it is a 2001 so replacing the u-joints may be needed.