I've tried this before and it isn't a good idea. All I can say is that weird things happen. Traditionally whole wheat flour makes much denser baked goods. A dense baked pancake is no bueno. Especially a dense German Pancake.
It pretty much defies the entire purpose of what you are trying to achieve here with your baked breakfast. If you are set on only using whole wheat flour, this may not be the recipe for you.