I just got done puting in usedrear axle assembly in my 1998 dodge 1500 4x4 5.2L spider gears where bad . When I am puting truck in driveor reverse clunking sound like something lose in my transfer case could the transfer case chain be bad or jack shaft be bad .

 

Mine does that too... Its because my spider gears are loose. excessive gear backlash can do it also.

You just got a worn axle assembally... thats why its better to just replace the bad parts, and you know everything is new.

 

did the clunking start at the same time you swapped rear ends ?
some clunking is normal, as its the slop in the drivetrain. some trucks have more than others. some rear ends have more than others.
could be transmission, transfer case, ujoints, or differential. if it just started at same time as rear end swap, then its likely that rear end.
can you put it up on jack stands and get under it while an assistant swaps gears. you should be able to track the noise.
i recently replaced my spider gears with a powertrax locker. it now has a LOT of slop when shifting in/out of reverse and drive.
is your new rear end 'open', or does it have limited slip or locker ? that could contribute.
if its in the rear end and its not really really bad i wouldn't worry about it.

 

I had rear axle cover off checked out spider gears before put used rear axle assembly in looked ok clunking sound seems come from my transfer case would be any back lash from tranfer case like chain or drive gear. I had truck up on jack stands put it in drive and reverse clunking sound fromtransfer case where drive shaft go in transfer case