Admin Menu Extra Items and Errors
Reverting the taxonomy view back to its original state, and then rebuilding the changes again made the errors disappear from watchdog, but the management menu and admin menu were still completely messed up.

To fix this, I installed Devel module, and the ran a SQL query to delete all menu rows added by system.

mysql&gt; delete from menu_links where module='system';


I then navigated to /devel/menu/reset 

This successfully re-built the management menu, and everything went back to normal.

Note: I also used backup and migrate to quickly clone the website onto a local server and test the changes before making the changes on the production environment.