Figured I'd update the thread for posterity for others. So I think my issue is resolved now. Dealer spent several hours trying to track down all my noises.
- They found some noise in the rear. Greased the back of the rear brake pads and replaced the retaining springs as they were rusting. Adjusted the rear e-brake shoes.
- Traced the pop to the front driver's side axle. Pulled the axle nut, which apparently was chewed up a bit from being removed and reinstalled 3 or 4 times in the truck's 160k mile life. Replaced the nut and retorqued and the noise was quieted a lot but still there. Dealership thought there was probably some damage in the outer CV, but suggested leaving it and waiting for it to get worse or start clicking when turning. I decided this noise has annoyed the ever living **** out of me and given how I treat the truck I asked them to just replace the driver's side CV. That eliminated the consistent pop at start/stop.
- There was still some other creaking/crackling noise and they also torqued down the chassis cross-member bolts around the transmission. I had done this to the torque spec (one side was low, probably from when the transfer case was dropped to swap the actuator) so I guess they tightened further.
At this point the noise appears to be gone. Whether it was worth $1300 to track it down and do all of the above, or if I should've just waited for the CV to fail more obviously for others I can't say, but I'm happy to have this behind me.
Since I'm at 160k I ordered a second CV from Serra Toyota in Decatur, AL. It feels like a decent insurance policy to have that on hand given it was $219 delivered. At some point I plan to swap the passenger's side CV as well, but it doesn't feel pressing at this point.