Okay, after reading the entire thread, these are my observations and recommendations.
#1 Try to avoid moving your fish so frequently. Not only does it stress them out, but the very act of netting them affects their slime coat and will make them more susceptible to disease. Adding salt to your aquarium is a good thing to help remedy this, as it promotes slime coat production.
#2 When medications indicate removing filtration, they are referring to any filter that has carbon in it because it will neutralize/absorb any medication you put in the aquarium. So if you're not using carbon, it's not a problem.
#3 I would wait a day or so before treating with any meds to give your fish a chance to recover. Withhold food for a day as well. If you're already using NLS pellets, pick up some Thera A and feed that to your fish about once a week to help digestion.
#4. Pick up some live bacteria and add some to your tank just in case. Because you've been moving your fish around so much, the last thing you want to do is stress them out some more with an ammonia or nitrite spike. Nitrate isn't as big a deal, and will be lowered when you do a water change. I would keep testing your water, and avoid doing large water changes unless your fish appear to be getting sicker.
#5 If your fish appear to still be acting up after a day, then treat with meds. Keep in mind, medication can be stressful for fish as well, so while you want to heal your fish, you don't want to overdo it either, so make sure you dose according to the instructions that come with the meds.