I thing I'd be most concerned with right now is giving more vaccines.
You're kind of in a spot because your pup needs to finish them, but it would be nice to figure out what is going on first.
On the other side of that, it sounds like while your vet is knowledgeable, they are moving way too fast.
The bile acids test isn't as accurate as we like to see until >20 weeks. And even then there are so many variables. The thing we do know about bile acids testing is that there is so much to learn about the test.
Any drug can potentially make them go up, so a vaccine could have falsely elevated it.