Tranny or transfer case or what?

I have a 1980 Cherokee with 360/TF727/NP208.  It would stop pulling while driving down the road in any gear.  A clanging noise started underneath and it would not go into Park with the engine running, it would only grind.  With the engine running it was clanging in every gear, including neutral.  I thought the tranny was bad so I swapped it out.  Now with the new tranny it will drive for about a mile and then the same thing happens.  I'm not sure but I think the noise is coming from the transfer case.  It makes the clanging noise in all transfer case positions, and it won't go into park with the engine running.  If I turn the engine off for a minute and put it in park, I can start it up and drive about a mile and it all starts over again.  The front driveshaft does operate in 4wd. If I put it on jackstands and put in in drive for a little bit it will do the same thing. Is it possible something in the transfer case is messed up?  I can't imagine two transmissions doing the exact same thing.  I'm stumped!  

Did you use the same torque converter?  

Yes, I used the one that came with the new/used tranny.  A buddy of mine with a lot more knowledge came over today and thinks it's the transfer case.  There is almost no resistance in the shifter and almost impossible to find neutral.  Probably the shift fork.  Some other forum replies on other websites seem to think it's the transfer case also. It seems to shift into neutral by itself while driving.