Did she end up getting spayed anyway or did you hold off?
I would personally be very concerned with an ALT 3 times the highest it should be in a Yorkie. I think the bile acids test will tell you a lot but even if it's not that, I would look for answers in other testing. Something just doesn't seem right.
Ellie's amylase was about that too and it went back up.
Her vet wasn't concerned either.