Table top collection (using the pee pad would fall into this category) is probably not going to work for this because so much bacteria can be introduced if they step on the pad before or after, etc. Then you may see a falsely high bacteria count. That isn't saying it never works but the vet may not want to take it by this method.
MVD (microvascular dysplasia) is small shunting throughout the liver. It is inoperable and causes high bile acids. The treatment is what you are doing now. The only way to 100% diagnose this is with a liver biopsy which they could've done during ls surgery. They can have both ls and mvd.
$4500 is just way too much for ls surgery. I'm just not sure Oakland has a good handle on this kind of thing. A second opinion wouldn't hurt and I'd be worried with the high bile acids and the possible UTI that there is another stones. You can always check with ultrasound or there may be ammonium urate crystals in his urine.
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