I have a 1999 2nd gen with 112,000 miles with 5 speed and 4x4 with some few upgrades. Considering trading with some difference of money for a 2005 auto 4x4 with 126,000 miles and all stock. What would be some good opinions and things to watch out for if I do decide to go the route of changing 

Private owner or dealer for the 2005? Find out how religious they were with and what fuel filters and air filters they ran and what trans service has been done. Pretty solid rigs overall other than I would want to know some details about the fuel system and trans maintenance and any history of issues. Probably due for Ball joints as well this is an issue the 3rd gens have the way the geometry of the axles are poorly designed but is minor.

wow a 1999 with only 112000, and a 5 speed, that's got to be worth something right their. if its a clean truck i've seen them bring in over 10,000 grand, A clean 2nd. gen is getting hard to come by.