Just read through this whole thread. Oh my goodness, you've been through alot. So happy Wiley went to a good Momma, and I'm sorry that your experience with him has been so rocky. The good news is though that, like a sick baby, it seems that you become even more attached when you nurse them back to health. My Gizmo was a puppymill/backyard bread puppy as well, however he hasn't had the problems poor little Mr. Wiley has had.
Glad you switched over the foods, Acana is a good food to be on.
I'm thinking that the hair loss could have been from all of the stress combined with the bad food and lots of medicatios that he's been on.
But thinning hair or not, he's a cute little peanut!!!
Prayers that all goes well!!! And lots of love a support to a fellow Puppymill/BYB rescue Momma!