The 3rd. gen 4x4 uses the same box as the 2nd gen. ? (Saginaw box on both, but is it the same?)
The 3rd. gen 2wd. 's use the rack and pinion as do the light duty 1500-2500 2x4 and 4x4.
The 3rd. gen 2500/3500 (4x4) hd's use the Saginaw box aforementioned. Its looks the same as the second gen (in the 2003/04 FSM), but I haven't pulled one to check for identical replacement etc.
Maybe call a dealer with a 2nd gen VIN and a 3rd. gen VIN to see if the number for the gear box superceeds to the same part #.
Good luck