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Well, aside from the bigger injectors and better turbo in the 99.5 and later 7.3's there's not a huge difference. They did some nice interior upgrades and the newer 7.3's (imo) have nicer interiors. Then there is the "mechanical diode" in the 01's. . .but i'm assuming most of those have worked out of circulation at this point, and the change to powder metal rods in 01.
What is your target price range?
I know i'll get flamed, but there are a lot of amazing deals out there right now on everything. . .diesels included. In 03 or 04 (can't remember the exact date) Ford started putting a dana 60 in the front vs the dana 50 that came in the older ones. The 6.0's arent bad motors (if you get an 06 or 07. . .they have the same heads as the 6.4 and don't have the HG issues of the earlier ones), and you can find some deals out there on the 6.0's. You'll also gain some ride quality w/the coil spring front end. . .definately a nice upgrade.
It really all depends on what you want the truck to do, and how you want the truck to do it. Left stock, you really can't go wrong w/any of the trucks. . .although, in stock trim a 7.3 will feel like it pulls a load stronger than the 6.0.