Okay.... After trying to find the info for LJ, I came across something I find a bit odd... the protocol your vet seems to be following is the same as for Copper Storage Disease, which can affect all dogs, but is rare in Yorkies, is normally associated with Bedlington Terriers. It is treated with prednisolone, every other day and treatment can continue for 6 months to a year. Additional biopsies are required to monitor the copper levels. L/D is low in copper and is food of choice, as these dogs also have problems associated with amonia (also in LS dogs) taking Lactulose will benefit them also. BATs are recommended.
This would explain the elevated AST and ALT values. Also read that corticosteriods will cause elevations in these liver enzymes (and can influence the BAT results). Usually with Liver Shunt, 3 or more of the Liver enzymes are elevated.
Not saying that your pup doesn't have a shunt, but there is definitely something else going on also. And one thing my vet did say, is that basically all liver disease is treated very similarly.
I agree with TLC though... why did't your vet look for a shunt while he was in there... but as more biopsies will be done, he'll have an opportunity to look again next time.... and intrahepatic shunts are found in large breed dogs (not that there isn't a first time).... probably not worth doing the BAT with her being on prednisolone as results will be higher than they really are), Gall Bladder sludge can cause problems too with test results and ammonia processing.
Also with the Metronidazole, some dogs don't tolerate it at all.
Definitely interesting case... Hope your baby is doing well and pulls through with flying colors!
Keep posting updates... I'll be watching....