I've been trying to do some research and figure out on my own but I havent been able to find anything. I have a 2006 3500 cc long bed and I found a cheap transfer case out of a 2007 2500 classic cc short bed. Are these interchangeable or is there a difference in the two trucks?

if the tranny is the same, or even the input spline count the same it will swap

they are all the same only difference is manual shift or electronic shift

Ok thats good then bc it is identical to my truck just it isnt a dually. Did gm fix the pump rub problem in the 07 classic or will it have that problem? I would like to fix it while I have it out if so.

no it was never fixed