reset your preferences
Immediatley after booting illustrator hold down shift, option, command
if that does not work a more aggresive rest of your other preferences.
move this folder to your desktop
/Users/(YOUR USERNAME)/Library/Preferences/Adobe Illustrator CS6 Settings/
Thanks for the response!
When I did the "hold down shift, option, command," it did allow me to click around in the program without giving me the beach ball of death, but I can't find things like toolbars (the option for tools doesn't come up in the Windows drop down.) Is that normal? Is there a way, in the weirdly sparse mode, that I can get things like the toolbars back? It did have warnings here and there about plug-ins being gone so I assme that means the reset was successful.
When I tried the "move the file" option, the problem persisted.