It all depends on what part you are looking at. A lot of parts are interchangeable 96-04. In 99, they changed up a few things, mostly cosmetic - so the hatch, grill, hood, and fenders are different. They also changed the front brakes, and the shock mounts... I'm sure there are a couple other things. I would say to be safe, stick to the newer ones.
As 180sx mentioned, they upgraded the engine in 2001. I am not sure what engine parts this effects.
I would think the interior is interchangeable, I've been inside both, and noticed next to no changes through out the years.
As for wheels, you can fit anything on a 99.5 - 2004, as they will be a minimum of 16". Some (most? all??) 96-99's came with 15's which may not fit over the larger caliper on your truck.