Jack up the bike, it only needs to have the rear tire about 8-10" off the ground. Remove axle, disconnect rear brake, slide whole tire to the right to release the rim from the gear splines. Clean splines and lube with moly paste (very important). and reverse process to put back on. Once the bike is up in the air, it takes about 10 minutes.
Shaft drives really don't have alignment issues. The hard part is getting the bike in the air. The 1100 motor hangs below the frame, so you either have to have a jack with adapters to grab the frame, or use a car jack to just get the rear wheel off the ground.
If you're at all handy, I'd invest in the motorcycle jack and adapter. You can make your own adapters out of wood, or just buy http://garage-toys.com/unmoad.html