Hi Rodger,
It certainly sounds like a complicated case you are dealing with for your Sheltie. Understandably, you’ve been through a lot of work so far but rarely are these cases simply explained or figured out. An ultrasound would be the next non-invasive step. Other than that, getting some biopsy samples would potentially more beneficial. There are pros and cons to getting endoscopic biopsies versus full thickness biopsy samples. I would suggest discussing this with the internist or consider seeking a second opinion.
Best of luck in getting this figured out to help your dog.
Dr. Ryan Llera