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I sold my 05 F250 today and planning my next build truck. I have for some time wanted to take a Ford SuperCrew DRW and build a sweet truck from ground up. This would include a Repower (Cummins-Highly modified), Real Transmission (still can't decide between a RoadRanger or a really built Ally Auto. ) Gut the interior (if donor truck needs that) New 19.5's and good rubber, etc... I mean a total rebuild.
I like both the 92+ Ford HD Body style and the 99-06 Super Duty body style. I am torn as to which to build from. Obviously I could pick up a 92-95 Crew DRW 4x4 for much less than I could a newer truck. However that newer truck would likely have a 7.3 (sell off if it ran good and recoup some of the build costs) and some nice added bonuses like Air Bags, etc.. for safety.
What besides Body style differences are there between the F350 DRW Crews (4x4) from the 92-96 era vs. the Super Duties of 99-06. I am referring to frame, axles, brakes, etc.... Are the two fairly comparable to each other in those areas? I don't care much about suspensions as the truck will end up with a full air ride similar to like my 05' did.
In either vehicle, a Road Ranger would be overkill. The pickup version of the Allison automatic is at best equal to or inferior to the 5R110W. There is no benefit in going with the light duty Allison. If you want a manual transmission stick with the ZF 6 speed. They put those behind the Power Strokes and the Cummins, so fitting it should be easy. If you want more than 6 speeds, throw a Gear Vendors unit behind the ZF in either an overdrive or underdrive mode, depending on your differential ratio.
I am also not sure I understand wanting to replace a 7.3L PSD with a 5.9L Cummins. The 7.3L has great potential for this build with a lot of parts available.
The 99-06 Super Duty trucks have much heavier frames and better brakes (especially the 05+ trucks) when compared to the 92-96 F-250/350 trucks.