The newer engine has an automatic cam chain adjuster and a more powerful lighting system. Further upgrades to the electrical system might be called for with the newer engine. This could be a psoitive thing, with a 55/60w halogen bulb replacing the older 35w incandescent.
This looks simple, but isn't. The wiring is substantially different, all the connectors are of a different configuration and different sex from one another, as are the regulator, safety switches, relays, component layout, brackets, wire lengths, etc. Without a complete LATE-model parts bike and wiring harness this can become an expensive, confusing conversion. The lever perches, for example, are drilled for a different sized tail light switch plunger, have completely different connectors to the harness, etc. It can be done, but it gets kinda ugly, with a lot of splices.
The good news is that you can transfer your existing electrical system and kicker over to the '03 (or even an '87) motor in about an hour, if you know what you're doing. Just transfer your sidecovers, stator, rotor, kickstarter and carb over to the new motor, plug everything back in and yer good to go. The most difficult part of the job being pulling the flywheels.
You could even recoop some of your munny by selling the late-model sidecovers, carb, stator, etc. on eBay.
I've converted both one-year '87's and post-'01 motors to the 90's system. Piece o' cake.