need transfer help asap

ok so this is my first post,im pretty smart on working on things and figuring out what is wrong,but i dont know so much in the 4x4 category,i have a 90 model 2dr,i recently put a new tranny in it,(the sorry ass puegot it came with),the tranny is good but the other day when i drove it for the first time when i would go to stop it was making all kinds of noise,not brake noise but driveline noise,so i put it on jackstands and in fourth and fifth gear there are alot of noises coming from the transfer in 2wd.so today i took the rear d.s out and ran it and the noise is a clicking sound with no d.s in it.with the d.s in it and u give it gas it makes noise like all hell is breaking loose.so what could be some causes of this,with the transfer in N and the tranny in 4th and 5th it has no noise so i know its in the transfer,any help would be much appreciated.

i have been thinking about this and my xj has around a 4-4.5 inch lift and the rear driveshaft has a moajor angle on it and u can see on the ears of the yoke where it has been rubbing the d.s.,im wandering if thats what is causing all this trouble im having,the guy i got the jeep from weighed alot more than me and that maybe why it never did it to him.does anyone have any thoughts on this?im gonna get some washers and longer bolts and drop the transfer down and see if it still does it.

No driveshaft in and it is clicking from the transfer case? Could be the chain slapping the case.

What engine? What was your build date?

ok so today i lowered the transfer with some spacers and it didnt help it.when u put it in 3rd 4th or 5th gear and give it gas the rear end is jumping alot the nose of it is.it has a 4.0 in it and the sorry ba10 pugeot.thats wut it came with and i just put a new one in it.the old one lost 2nd gear.today i stuck my finger in the transfer and the chain isnt that loose,it makes the noise in 2wd.it sounds like all hell is fixing to break loose.i can put the transfer in neutral and shift every gear with no noise can take the rear driveshaft out and it makes a clicking sound in the transfer.i dont have any idea what is causing this noise and horrible vibration.the tranny i put in it is used and the warranty is fixing to go out on it but i dont think its the problem.it amkes no noise with the transfer in neutral so thats wut has me so confused.i need any help someone can give me at this point.

it deff sounds like a chain prob to me. i have had a chain slip and pop and to "feel and sight didnt seem loose.