I'm actually thinking M with auto-ISO might be the way to go in the future
Any reason not to use shutter priority mode? That's exactly what it's for. Leaving auto ISO on is fine to give you more range than your lens is otherwise capable of as well.
Both camera shake and motion blur should be almost non-existent at the shutter speeds and focal lengths you are using. Out of focus blur and camera shake look fairly different as well.
Autofocus depends on both the camera body you are using as well as the lens. If your gear isn't up to the task an option can be to use focal depth range and time shots that are happening at your preselected focal ranges.