Could I swap in a tranny and transfer case out of a 2500 series truck into my 3500 without too much trouble? If so what problems may I encounter? Can't find a used transfer case for mine.

No difference in the Auto tranny's from 2500 to 3500 same 4l80E. Some 3500's had a borg warner transfer case. Some 3500's and all 2500's had a New process/ New Gear Vendors (241 I believe). The Borg Warner has a magnesium case and is supposed to be more heavy duty. Depending on how hard you plan on four wheeling the New Process should be fine. There might be driveshaft length differences if you change transfercases, but I don't think so.