I am not fond of using Servo focus unless I know my subject can be moving.   I use Nikon but suppose Canon's does the same thing.   The lens keep trying to refocus and it is easy to snap off a less than sharp image.

Agreed with Danny and others to get comfortable with the 400 before trying to up the magnification..that is leading to problems you are not ready to handle without practice with the lens as it is.   The 400 will give you more available aperture(light gathering ability) and therefore faster shutter.    

I also prefer to shoot in Aperture priority though others will differ with me on that.   Critters take a reasonable fast shutter unless they are sleeping or quite still.

Even with a tripod 400 mm is 8x magnification and some shake can come through. Wind can do it, body motion can do it..craming the shutter instead of a gentle push can do it.  With the extenders the problem is greatly magnified..no pun.  

If the subject is still or will stay in frame, you might focus, move your head from the camera on tripod, cover the viewfinder with a finger and push the shutter. This is not for action shots but will help prevent body motion from moving the stuff when the image is clicked.

The diopter on the viewfinder will let you adjust your shooting eye to what is Really in focus.  I wear glasses and must look through the same part of the glasses for each shot in manual focus.  Developing a personal "hold" on the camera when using mf is likely a good idea..repeat the same each shot and it becomes a habit.

Personally, you will learn more by not using the special settings for portrait, landscape, etc., whatever the Canon has there.       

Best wishes.          TomDart.