Maybe put him in a certain place to eat, with a floor space that is easy to pick up. We like commercial entryway rubber-backed rugs we buy at Sam's Club, to put around on the kitchen floor and avoid slippery spots. After years of having dogs have periodic problems walking on that bare floor, we finally came to that happy conclusion. It's safer for us, too.
So I wouldn't put him on a bare, slick floor to eat, but perhaps some rubber-backed rugs. Some dogs do like to remove their food from the dish to eat it. It seems to be instinctive. I would not make an alpha issue out of it.
I had one dog who seemed to have a need to carry her food off and "hide" it to eat later. For quite awhile, I gave her BilJac frozen dog food, thawed in the refrigerator and then formed into a ball--just handed it to her! She would take it someplace and hide it. I didn't want the bigger dog to find it, so I'd ask her to show me where it was, and she learned to do that. Then she would go ahead and eat it.
This was a brilliant dog, by the way. She was also highly trained, and working with her on her feeding contributed to my ability to work with her on everything. Your dog's eating is an opportunity.
I asked my vet about our young Standard Poodle Worthy's eating, whether I should be concerned that he doesn't eat quickly. We had multiple dogs for so many years, and now have just the one, my assistance dog for mobility disabilities. The vet said it is normal for an only dog to eat more slowly. And sure enough, we have to watch his weight to keep it from getting too high!
I do take up the food if he doesn't eat in a reasonable length of time. I recommend you do that, too. Food sitting out too long causes various problems. If you start taking it up after awhile, he will start eating more promptly.
Do watch his weight. German Shepherds can have a problem with being underweight, especially when young. And the bowel problems are not unusual, either. If you want to change foods, the intestines need time to develop the correct friendly bacteria to digest the new food. I'd suggest you take 2 weeks to make the full change. Start with 25% new food, 75% old food for a few days. Then go to 50%/50% for a few days. Then go to 75%new/25% old for a few days, and finally go to 100% of the new food.
Another thing to try is probiotics. We give multidophilus that we buy at the health food store. It needs to be refrigerated there and also at your house. These are the friendly bacteria that help avoid diarrhea from a food change. They are also very, very important whenever a dog goes on antibiotics, which will clean out the friendly bacteria on my dogs every time. So I always give probiotics too.
I have heard of German Shepherds having their puppies in a den dug out of a hillside! I think their instincts are strong. That is not a problem. You may well find that the dog's way of eating will contribute to training, and GSDs absolutely need lots of training.
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Kathy Diamond Davis, author, "Therapy Dogs: Training Your Dog to Reach Others," 2nd edition, and the free Canine Behavior Series articles at http://www.veterinarypartner.com/Content.plx?P=SRC&S=1&SourceID=47