There are only a couple of major differences but the parts differences do add up to quite a bit. In '98 Honda started putting the JDM ITR 4-1 Header with 2.5" Collector onto the TypeR motors. The '96-'97 motors got a regular cast manifold. The header by istelf is not uncommon to sell for around $400 if you wanted to upgrade from a cast manifold.
The other major difference is that the '98+ ITR's got the 4.7 Final Drive in the transmission vs. the standard 4.4 that the '96-'97 ITR's got. Again, the price of the parts is alsmot $350 for the Final Drive kit if you wanted to upgrade a standard transmission.
Neither motor will be harder to install that the other. If you do get the 4-1 Header, plan to go to an exhaust shop or roll your own, since the standard size inlet on honda catalytic convertors is 2.25".
Other than that, just match the correct year ECU with your car, or you may need to get a jumper harness. 96-97 Honda's = OBD2a, 98+ = OBD2b. The 2 OBD systems are interchangeable, just the plugs that go to the ECU are difference, hence the need for the jumper harness.