Well, apparently, Yoda caught a parasite somewhere (from either drinking bad water on a walk or eating grass we think) and that's why he had the diarrhea. Also, he had flea bites and that's what he was trying to scratch. The doc gave him some steroids (muscle Yorkie Yoda coming soon!) and some medication for the parasite (though that has probably passed through his system by now).
So, just be careful out there if your Yorkie drinks from yucky puddles of water! And be careful of grass as well! He seems fine now, full of energy and quite the appetite!