After some extensive testing I believe I have come upon a solution!

I uninstalled the mod because it was broken, and reset the cells using the 'resetinterior' command. I did this for the three halls, the arcaneum, and the arch mages quarters. I then noticed that the door to the mage's quarters was missing in the Hall of Elements. I was annoyed but I figured it'd be better to have a missing door then to not be able to get access to the Halls of Attainment and Countenance.

A bit later I figured it wouldn't hurt to try the updated version, I was running on 2.0 I believe. and now there's 2.51. In my first attempt to use this mod, the door problem occured with the college's bar inaccessible due to the archmage quarter's door in the way there. A new game that I started JUST to play this mod resolved that issue, but the door itself stayed gone after I uninstalled. I decided to try the updated version since the door problem wouldn't occur as the archmage's quarters door was allready missing in my save anyway. So I reinstalled the mod, updated version, and applied the door fix patch.

To my relief I was able to enter the halls of countenance and attainment again. BUT, when I went into the archmage's quarters, I got the infinite load bug. 

I realized I had reset all of the cells, and entered them all to see if they were working when I uninstalled the mod. All of them, but the archmage's quarters. And that was the ONE room that wasn't working with the mod reinstalled. So I did an experiment. I removed the mod again, reset all the cells once again, then entered each one to initialize them, including the archmage's quarters, saved, reinstalled this mod, and now -everything- seems to be working exactly as intended. 

My conclusion to this is that you need to not only reset the cells, but initialize them by entering them at least once (however briefly) before installing the mod again. Once you do that everything should be fine and you will be able to enter the halls, arcaneum, etc once more. Just make sure you reset them all with the 'resetinterior' command, then go into EACH ONE before saving and quitting to install the mod again.

I believe this will solve most people's problems, and i'm relieved to have it all back and working. This was just an accidental discovery due to trying something on a whim, but i'm glad it happened. I hope this process helps!

To summarize:
- Save your game somewhere outside the college
- Remove the mod
- Start the game and enter an unrelated interior (I used Birna's Oddments because of it's proximity)
- Use the 'resetinterior' console command for the Arcaneum, Hall of Attainment, Hall of Countenance, Hall of the Elements, and the Archmage's quarters
- Use PCB to clear your cache to make sure fresh 'from scratch' versions of these cells will be loaded
- Enter each of the cells individually to initialize them ALL. Don't mind the missing Arch Mage's Quarters door in the Hall of Elements, this just means when you reinstall, The college bar will be easily accessible. Enter the Archmage's Quarters through the Arcanaeum, instead. 
- Save in the courtyard
- Reinstall the mod and start the game
- Load your save in the courtyard
- Check each of the areas to ensure they load properly, enter each.
- Do the Happy Mage dance as you find everything working like it should! For bonus points, conjure a partner.