Ryan, I have the Canon Pro 2000 model and after about 18 months the printer started to exhibit sounds similar to what you have described.
Canon replaced the purge unit and pump under warranty which solved the problem. It took the tech roughly one hour to replace the unit. However, in the process 200ml of ink was purged so you would need to makes sure the maintenance tank has enough capacity.
Canon Australia wouldn't come to the party in replacing the lost ink, although my dealer did. Canon does not cover consumables used during a service which frankly is
poor policy on their part.
From what I can gather the purge unit is a known issue with the Pro 2000-6000 models.
Hope this is of some help.
-David