Should I be putting peroxide on all those sensory pits at this point? Or is that going to cause problems?
Sensory pits can vary between individuals. That said, I tend to agree with Ryan that it looks like there's been some erosion, but I've certainly seen much worse. Once it's cured, fish can live comfortably with much worse scars than that from HITH, so (once cured) it's more of a cosmetic issue than anything. Personally, if I decided to do the swab thing, I'd do just the recently infected spot, not much to be gained with old spots that were cured a while back imo.
I agree with Ryan on the netting thing and will add that the amount of stress varies, partly by how you go about it. Put a fish through an ordeal of chasing him all over the tank before you actually catch him increases stress, so if a fish is elusive or difficult to capture I'll either drain the tank to make it easier and/or use something like an expandable window screen (which I also use as tank dividers) to gently shepherd my target to one end of the tank, easier on both you and the fish for netting. Some fish are better about being netted than others, some become accustomed to your presence in the tank (water changes, rearranging, etc.) or to handling, so netting them gently isn't much more than a minor nuisance for them. Other fish are more sensitive about it, but typically recover in a short time if the process itself was reasonably quick and gentle.
Now, regarding fish digestion, here's a scientific fact: Stress affects fish digestion, in part by taxing their energy budget, but also by producing stress hormones (cortisol). This can affect digestive acid secretion, enzyme activity, intestinal wall cells. Another point, "it has been demonstrated that antibiotics heavily modify intestinal microbial populations, and that after treatment with antibiotics, individuals are more susceptible to infection by pathogenic bacteria..."
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3344833/
Because of this I tend to feed fish lightly if they're highly stressed, sick and/or being medicated. I'm also suggesting that sometimes the digestive abnormalities people see during or after fish illness and treatment with meds can be due to stress and the effect of medications and in some cases where people interpret this as the fish is still sick and needs more meds, they are perpetuating the problem. I'm not saying this is or isn't true at this point with your GT, but it's a possibility and it could be a rest from meds is needed and would improve his digestion.
I'm probably going to get pushback on this, given your fish's history and everyone's varying personal experience and zeal to be helpful here. So-- again-- I'm not there with your fish and haven't been there through the whole ordeal, so this isn't a diagnosis on my part and I'm not advising you what to do next. But it's a possibility that, given my background, personal experience, and philosophy in keeping fish, would influence my next steps, unless I was seeing something additional to convince me my fish is still sick-- in other words my preference would still be to rest him a bit and see how he does before jumping right into more meds-- just my opinion.
