Have the fixed it? Well my character is not getting well rested bonus and it keeps tallying the days as warewolf even after I cured myself. Please fix this bug been looking anywhere for anything that can fix the days of warewolf and well rested bonus so if anyone has any ideas to help me fix it myself please let me know. Also in a Wiki it says you can use a console command? What console command?

From http://elderscrolls.wikia.com/wiki/Werewolf under Skyrim Bugs:
Sometimes after you cure yourself from the companion quest, you will still will have the side effects (No "Well Rested" perk and comments from NPCs) of the disease but not be able to transform. The player can use the following console command to partially fix this (the counter for werewolf will be stopped and the player can get "Well Rested" perk. However, the NPc still comment about the "Fur from your ears").