2003-2004 no emissions, nv5600 trans, possible valve seat problem if run hot.
2004. 5-2007 catalytic convertor, g56, dual mass flywheel, improved valve seats
2007. 5 and up has 6. 7 with all emisions, g56, factory exhaust brake.
2003-2004, correct info. 3 versions SO (250/460), HO (305/555), and Cali (235/460).
2004. 5-2007, 04. 5-05 had a NV5600 and standard flywheel, 05. 5+ has DMF/G56. Emissions were done mainly with timing, but also piston design. 1 version, HO (325/610 (600 in 04. 5 if not flashed))
2007. 5+, correct info. 2 versions auto (350/650), manual (350/610). . 350/800 HO for auto's should be available any day now.
Some additional info. All 5. 9's in 3rd gen's have the same camshaft grind, which is very restrictive on the exhaust side and has no/minimal valve overlap to have an "in-cylinder" EGR effect. With the piston change in 04. 5 the EGR effect was increased, which is why 04. 5+ trucks respond better to cam swaps than 03-04 trucks. The injection timing was retarded in 04. 5+, and a 3rd event was introduced to reduce emissions, this can be advanced with a tuner. The turbine section on both the 03-04 and 04. 5-07 turbo is quite restrictive, which increases back pressure and reduces airflow, in turn aiding in the "in-cylinder" EGR effect.
Again 04. 5-07 have the main "in-cylinder" EGR, but 03-04 has some commonalities.
I am quite happy with my 05, but have also swapped the cam, turbo, and added a tuner. . but the blasted piston design still keeps my oil dirtier than an 03-04.
Maybe with EFI Live on the horizon it will help removal of the 3rd event and improve tuning for all the tuners, a little competition is a good thing!