I know at least one difference is the ignition system; the 98-00 uses coil packs with wires, while the 01-04 uses a coil on plug design. Not sure if the new style will plug into your harness without issue. You might be able to swap over the old coil packs and wires to the new engine, but you would also need to move over your old valve cover. The intake manifold design also changed where it bolts to the head, from 8-port to 4-port (most used engines come with intake manifolds, so this is likely not an issue). Also, the new engine may have the 315cc pink top fuel injectors, which are more desirable than the 300cc brown top ones, especially if you are considering forced induction in the future.
If the new engine comes with its exhaust manifold, it will likely be the updated mini-header; even if it doesn't, I recommend the upgrade to avoid the cracking exhaust manifold issue that plagues so many people (unless you plan on turbocharging in the future). You also get a bit of a power increase, from what I've heard.