1. Any suggestions regarding the possible bloating? No - as I understand it, the YT is eating nori well? That would reduce constipation. Ascites (fluid build up) can also cause bloating, but the root cause of this is liver or kidney disease and not really treatable.
2. Should I be looking into antibiotics? In Canada, we need prescriptions, which can take a bit of time. I have found a good vet, but depending on what I'm looking for it can be difficult. They had to special order in the Praziquantel. I was leaning that way, but I think I'm reading here that you backed off on the copper and the breathing got worse? That's a bad sign, if copper toxicity was present, it should have gone in the other direction. Still, antibiotics could be warranted, but you being in Canada leaves me at a disadvantage as to what to suggest.
3. I have two small clownfish in nursery boxes in the QT. I would say they are pretty happy. They don't show any visible problems/symptoms other than the occasional flashing. Are they of any concern/risk being in the same system as the YT? Perhaps, but that's a done deal now that they've been in there.
Maybe you could try a test FW dip on one of the clowns? A single prazi dose like you did will not treat egg laying flukes, as any unhatched eggs will then hatch out after the prazi has dissipated.
Jay