That is a lot to take in.
First, I question both vets.
An intestinal biopsy/endoscopy couldn't have shown liver shunt and just because the liver enzymes are normal doesn't mean a thing. The liver has to be considerably damaged for the enzymes to go up in most cases. Was that 79 the pre or post result?
Before I forget, when feeding wet food it has to be converted to dry matter basis, so it isn't 8% protein. Take the protein and divide by the recipracol of the moisture. So if the protein is 10% and the moisture is 80%, 100-80=20. 10 divided 20 = .5. So the protein would really be 50%.
Ultrasounds are only 60-80% accurate at diagnosis shunts and with a number like 79, it is likely microvascular dysplasia (small shunting throughout the liver). This is treated be supplements and diet and can't be surgically corrected.
He may be a picky eater because if he does have LS and MVD, toxins could be building up in his system and wouldn't be properly filtered by the liver. This would make him not feel well. The type of protein given and the amount is extremely important.
If a shunt is suspected, why would a vet do exploratory surgery?
The only surgery that would be needed (as far as the liver goes) is an ameroid constrictor placed to close the shunt. This is if he has a shunt at all. Bile acids can be up for any liver function issue. If that is suspected though, a Protein C test is next followed by scintography. Ultrasounds are good if bladder stones secondary to liver issues are expected or if the vet wants a look at the abdomen.
Is he on supplements?
A liver compromised dog should go on prednisolone, not prednisone, as far as I know. IBS and liver issues go together sometimes.
What is being done about the bacteria and what has been tried?
Is he on probiotics?
Why does the vet think it is liver shunt just because of high bile acids?
Are they sure it isn't secondary to the food poison/high ALT issue?