Sosoconfused - You've spent years and years educating yourself to be a good JW, and all the meetings, assemblies, CO visits, have just hammered it into your mind like a board that has hundreds of nails pounded into it. It will take time to pull all of those "nails" out.
Educating yourself by means of reading books like Steve Hassan's and Crisis of Conscience and websites like JWfacts will go a long way toward combatting the guilt you're feeling and freeing your mind at the same time.
Don't lose heart. You'll get there!