+1 on FoCal.
There's a DIY solution here: http://www.the-digital-picture.com/Photography-Tips/AF-Microadjustment-Tips.aspx
+1 with Neuro on FoCal. It will be a great tool if you plan to add more lenses. DIY kit takes WAY too much times.
Call Canon and tell them you want to make sure both camera and lens are perform at best level. I doubt they will charge money for this task, since you spent over $5k on their product and both items are still under warranty.
Canon will adjust your lens to match a reference body, and will adjust your body as well. If you have other lenses, or get them in the future, you will be asking the same question again.
FIRST, check to see if you need a adjustment. Put the camera on a tripod, focus on a flat wall with Detail and snap 10 images at the widest aperture resetting the focus to infinity between shots.
Now, do the same using live autofocus while in liveview. Unless the liveview focus is noticibly better, you do not need to do anything. You should try at varying distances and zoom settings.
You can put two different AFMA values into the camera for zooms, one for minimum zoom, and one for max zoom.