Michelle, the reason I asked about his blood count is because his symptoms sound a bit like possible PLE. You see GI symptoms and the blood work often shows protein loss. (You mentioned something in the blood being low) There are four causes of PLE and IBD is one of them. When there is inflammation in the bowels, the only true way to diagnose is with a scope and biopsy. Here is a link with information:
Intestinal Lymphangiectasia
My Cookie has PLE...she has both lymphangectasia and IBD. She has been stable for a bit over 3 years now. I was fortunate to catch it early...the protein loss was the key and my vet suggested a specialist who did a scope and biopsy. So, we knew exactly what we were dealing with.
I hope that you can find out exactly what this is quickly and get Couver on the road to recovery. It may just be IBD, but if the blood work showed something...I am wondering about the protein loss.