Well, that's good. I am glad they are in touch and discussing his case. The reason I suggest specialists is that, in my experience, they usually have a diagnosis in a day or two. They don't look for one thing at a time. It is pricey but in the end, they get to the bottom of things quicker. They take a thorough history and make a list of all possibilities and start testing. It doesn't mean that a vet isn't good...it is just that the specialists see more weird and/or complicated things.
That UTI probably did occur during the neuter....if you read about UTIs in male dogs you will see it just isn't a common thing.
The bile acid testing really is a stretch. It was just "a thought". They may think it is simply not necessary to do.
Hopefully, it will all be figured out quickly and Frodo will be on the mend!!