I ran into this issue as well. The hinges on my passenger door were clearly replaced at some point because they are bolted in. What size drill bit did you use for each bushing on the lower hinge? Not sure how tight to make it since they are press fit.
Does anybody else have a saggy 3rd door (cargo door/whatever you want to call it) on the extended cab? I think I found the parts but they are all discontinued. I'd probably need a couple of each.
Rear Door
15704627 - Door Hinge Pin
15708060 - Door Hinge Bushing
15708061 - Door Hinge...