Unfortunately this is the nature of the beast. Mine started the clunk at around 40K miles. Over the last 18 years of ownership I have replaced a fair number of parts including both gearsets, entire front diff carrier, rear driveshaft, and front drive plates. None of these cured the issue. I haven't replaced or rebuilt the transfer case, but this hardly seems worth it as a brand new one started clunking after 40K miles. She now has 203K miles.
The only way I've found to quiet the clunk; keep the slip yolks and universal joints properly lubed and turn up the radio.
The only way I've found to quiet the clunk; keep the slip yolks and universal joints properly lubed and turn up the radio.