Good evening everyone

I could really use an ear and some advice with for dealing with the Tobester (or maybe you need to just talk me off this cliff?) So if anyone has time to read my novel, and let me know what they think, I'd be so grateful.
My Dober-boy is 8.5yo, and he's been moving towards hypothyroid since the spring I think (hindsight is always 20/20.) When I look back at his spring vet records I see that his thyroid was at the low end of normal, and his cholesterol and triglycerides were creeping high. All good indicators that maybe I could have started him on meds then, but... I didn't look that close at his test results. Bad mom.
About six weeks ago, he needed minor surgery and that is when it all started going awry. First he had a reaction to the sedation. Then he had a reaction to the antibiotics, and his ALT shot up to 500+. He was vomiting and miserable, and the vet switched him to Hill's ID, which he has been tolerating fine since. But as we starting switching back to his regular food (Wellness Core), he stopped acting like himself, and started losing weight. He's always been a "hard keeper" and a really heavy drinker (which the vet has not been concerned about before, but has been watching).
So a week into food switch (yesterday), we retested everything, and did abdominal X-rays, which were clean. The radiologist thinks that everything looks normal. His T4 is only 0.7, I'm still waiting on the Free T4 test results. ALT is back to normal at 47. Cholesterol and triglycerides are still high, Amylase and CPK are low end of normal. The vet thinks that this is *likely* just hypothyroidism, and that the liver involvement is due to the low thyroid levels. I'm worried that there may be another issue here that I shouldn't be too eager to write off.
So enough rambling background, on to my questions. The vet wants to start him on thyroid meds ASAP, which I'm going to do. Do I give the thyroid meds 6 weeks and see if any of the liver symptoms resolve or do I continue to try and hunt down a cause for this intermittent liver distress? Should I ask if we can start a supplement like Denamarin? I'd really like to avoid feeding the Hill's ID, and the vet is recommending that I feed something with less protein and fat and more fiber in it than the Wellness Core. Does anybody have any recommendations of similar quality to the Wellness that I can run past the vet for approval? Until then, he's back on the ID.