So I was able to do the quest and I'm the arch mage, YAY, but there is a problem. I may just not be waiting a long enough time but after a couple days, my magicka still won't return to normal. Ever since the staff was used on me I have -65 magicka without my equipment but 80 with it, I should have around 280. What should I do? If it's a glitch is there any command I can use to fix it, if it's permanent than I guess that sucks because I was playing a pure mage. If it should slowly come back that would also be nice to know.
Check your "Active Effects" section of your character. Anything highlighted in red represent the bad/negative effects on your character. If the Staff of Magnus effect is still there go to any of your owned beds and sleep for a 24 hour period. Then return to the arch-mage.
If the problem is not a staff and a serious disease/poison or injury. Use the appropriate potion of "Cure Disease" to cancel the effect.
If the effect is a class effect (like becoming a vampire) you'll have to do a specific mini-quest in order to have the curse lifted.
You can also remove all negative status effects by going and praying at any shrine you'll receive a blessing from that deity. If you have Hearthstone you can build some in the basement of your Manor outside of Falkreath.