You should be fine just draining the fuel from the carbs. When you remove the petcock inspect the screen and standpipe. If they're good you shouldn't have gotten any rust into your carbs unless you were running on "Reserve". BTW do not clean the tank with the petcock installed. Remove it and clean it seperately.
With the petcock in the "On" position you are getting fuel from the tank through the standpipe. When the fuel level drops below the top of that standpipe you "run out of gas". When you switch to reserve you bypass the standpipe and access the remaining fuel in the tank.