This is a timely discussion, as I am in the same quandry. I have an '06 with the G56 AD that I bought new. In 2011 with 103k on it, I lost 4th and 6th gear. The truck has basically been sitting for 5 years now waiting for a transmission. It looks like I'll finally be able to get it back on the road soon using tax refund money. I'm on the fence as to what transmission to go with. If I only get another 100k out of a G56, I don't want to go that route. The NV5600 is an option. But I've also been considering a ZF6. For those who aren't familiar with it, this is an aluminum cased 6 speed transmission found in the later model Ford diesel trucks. I recently put one in our family vehicle (a 2003 Excursion with a 12valve P-Pumped twin turbo Cummins), and was really impressed. It shifts great!!! Even with a SB double disc clutch, the shifting is smooth and quick. The case is HEAVILY gusseted externally for reinforcement, and it incorporates a pressurized oiling circuit with an integral oil pump. There are transmission lines in/out to send to a cooler and external filter.
In light of the original discussion, if you are going to stay ONLY at stock power levels, maybe the G56 is an option. I had replaced my DMF with a solid flywheel from southbend and a new clutch, and always ran Amsoil ATF in it. It never did shift as smooth as the ZF6. I also was running 35" tires for about 2/3 of the miles, and 37" tires for the other 1/3.
IMO, I would opt for a '05 truck with the NV5600. Or get an '06/early '07 recognizing that the G56 is the weak link.