Did the vet do a biopsy while he was open?
Borborygmus (stomach rumbling, intestinal noises) can be a sign of IBD. You would need a biopsy to know for sure or to see if it is something more serious. With all the throwing up, it may be something else. In cases of IBD, it can be good to use omegas 3s as their linoleic source. Has the vet tried Metronidazole or Tylan?
A homemade diet is great but you may want to make it grainless and a novel protein should be used (maybe whitefish?).
Probiotics may work for some dogs.
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