Ok, let me see if I can explain this as I figured it out by accident. If you sign out of your iCloud account under iCloud in System Preferences, it should prompt you to sign out of the same account in Mail (or something along those lines). It will ask if you want to keep or delete things from your Mac ... just agree to it until you are signed out. Then sign back in under iCloud in System Preferences with your MobileMe username and password and go through the set up again. I was then able to link my mail and contacts and everything is working the way it was before except under an iCloud account.
Hope that makes sense. Like I said, I figured it out by accident.