If you were having a problem before than I would say it's your linkage. A lift and transfer case drop are a definite case for out-of-adjustment linkage. There are a few good write-ups on how to adjust your linkage on this and other forums.
If it will make you feel better, just disconnect your linkage and shift the transfer case by hand and it will prove where the problem is. After a lift, tummy-tuck, and manual to auto swap, I gave up adjusting the linkage and just went to a Novak cable shifter. No more problems with 4lo.