Even before looking into physical items, check your tune. I have the same problem after
tranny work. I swore it was the rear gears, because I changed to 3.73's shortly before that. Turned out to be the tune screwing with the shift pattern. First, make sure you have the correct gear ratio programmed in. Second, make sure the tune is correct for the
tranny. If there is even one aspect incorrect, the transmission will be totally confused and will be really clunky and constantly hunt around for the correct gear. If neither of those are the problem, then start looking at other items like those listed above, but I would always work backwards from the last modification.....