I have completed the mage quests and become the Arch Mage. I used to have access to my own private room at the top of the tower, however the pad in the lower lobby no longer sends me up a level. Whats up? I have not completed the main quest yet and now I do'nt have access to anything I stored up there?

Any mods relating to the Arch-mage?

No I am playing the game in it's original config.

Can you enter the rest of the university? you might be expelled because of a crime against the guild like hitting a mage or even your horse.

Yes that's no problem.