You guys have been so helpful - I wanted to post a quick update on our rescue, Buddy.
On the medical side, we went forward with an endoscopy a few weeks ago, after further tests and an ultrasound showed issues, but nothing conclusive. In the words of the vet, "It looked like a massacre up there." He had some bleeding ulcerations (sorry if that's TMI) and a lot of areas of inflamation. When the test results came back, it turned out to be primarily an embedded e-coli infection of the large intestine. There are some other issues as well, but the vet didn't think that those were worth worrying about. We immediately put him on a super dose of Baytril...and his pooping improved almost instantly. What an amazing difference - and he's been accident free in the house (except for the submissive peeing) since then. Poor little guy - god only knows how much he was suffering before we figured out the right treatment. I'm really glad we chose not to be satisfied with the diagnosis of "nervous colitus" - regardless of the cost. He'll be on antibiotics for a while now (we're adding pre and probiotics to his food, as well as an iron suppliment to help him recover from all the blood loss) but things are looking up.
On the behavior side, he's making major improvements. He's slowly becoming more social and confident, although he's a work in progress. We've signed him up for a basic obedience class with our trainer, and once he knows the ropes, I think we'll try him on some beginner backyard agility. He's been doing so well with recall we've been giving him a lot of off leash priveledges in the "safe zones" (we live on a large farm surrounded by woods, so there are some remote areas and trails where he can be off leash without worry) and he absolutely loves it. He and his sister Lucy go crazy every morning running in circles around me on our walks. I posted this in a reply, but this is a video of the two of them playing (Buddy is the red merle):
That was a few weeks ago, and I swear they're at double speed these days. He's such a happy boy all the time - he loves cuddling in bed with us and loves playing with his sister. He has CRAZY energy though - I read that post about zoomies and had to laugh. When Buddy's excited he spins in circles and jumps straight in the air - he can basically get up to my eye level.
So, I guess that wasn't so quick, but things are looking up!
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Re: Buddy update
What a wonderful update!!!!! I'm so happy to hear that you got some answers on his health issues and I hope that the new treatment plan helps.
And he is making great strides! I'm sure he would love agility and it would give him some confidence. I know that Jackson make a HUGE leap in his socialization once we started playing disc, even before we started competing.
You guys are doing a great job with him and I look forward to even more updates
After working with a feral herding breed dog I have a super soft spot for Buddy 
Poe: Here we go once again with the "I was a wild stray..." story. Blah blah blah *eye roll*
Blog: The Misadventures of Jackson and Poe