Had the same thing happen two weeks ago. Here is what I did:
1. Remove all exhaust parts and dump the water out
2. Remove air box and dump the water out
3. Remove the carbs and dump the water out. I took them completely apart, rinsed with isopropyl alcohol (rubbing alcohol), then sprayed everything off with carb cleaner. Left them apart to further dry while I did the rest of the steps.
4. Pulled the cylinder heads and cylinders.
5. Using a small hand pump with a thin piece of tubing, I pumped the water out of the crank case. Then I filled the crankcase with rubbing alcohol, pumped it out again and repeated once more. I then sprayed a bunch of carb cleaner in the crank case, then set a big fan on top of the engine blowing into the crank case for a few hours. The puropse of the alcohol is to remove any traces of water. Water and alcohol form what is called an azeotropic mixture which means that they blend completely (unlike gasoline and water which seperate) and will evaporate at a much faster rate and lower temperature than water alone.
6. While the fan was running, I drained and flushed out the gas tank, oil tank and cooling system. I used rubbing alcohol in the gas tank and tried my best to spray it all over using a squirt bottle. Then I did the same with gasoline to rinse out the alcohol. Make sure that you get all of the fuel lines rinsed out too.
7. Drained, flushed and refiled the chaincase.
8. Using the hand pump, empty the water out of the trunk!
9. Regreased all suspension and steering parts.
10. Your speedo cable is probablly broken if you pulled the sled around after it had frozen up... mine was broke.
11. Put it all back together.
12. Cross fingers
13. Pull on rope and hope it makes fire!
14. Mine started on the second pull. Project took about 6 hours with two of us working (lots of beer breaks!). I have put 250 miles on since the incident and it is running as good as it ever has. Gotta love Yamaha!