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For the most part there are all very similar at the core. Early 99's (build dates before midyear 98 I think) have a smaller turbo, a slightly different intake, and a 15 degree HPOP versus the 17 degree in late 99 on. Depending on engine serial numbers somewhere around mid 2001 models have PMR's (Powdered Metal Rods) as opposed to the earlier models having forged rods. Those are the slight differences in powertrain I can think of right now. Creature comforts are getting kinda nice in the 2002 models. But essentially the same rig IMO.
The reason I'm asking is because I'm looking at a 1999 F-350 with the 7.3 that was sold on 09/09/1998. I know the consensus of the 7.3, but will I be running into any trouble with the 7.3s in the 99s?
If properly maintained, you will not have anything in the early build dates that will cause any more "trouble" than another build date, plus if you want to update it to a late version RiffRaff has everything you need to change it over Riffraff Diesel: Early/Late Conversion Kit. Personally I would just run with it as is. It all depends on your goals. One thing I forgot too is the early 99's have slightly smaller AB code injectors, which flow a little less fuel.