There are actually a lot of differences over the years in cummins engines. Yeah, the core engine and some components remained somewhat the same, but if you're looking at swapping, you're better off getting the same year engine.
For instance, most don't know that they changed the way the cam/crank timing is picked up in 2000.
Let alone changing from a vp44 to common rail in 2003, then adding egr and changing the cams in 2004, and going to a 6.7 liters in 2007. Plus the addition of different families of exhaust filters and catalysts has occurred since then. There were quite a few changes that most don't know about.