Yes it is critical to try and get them into QT .. This will allow you to control every aspect and try to get the treatments they need , it also makes it easier to remove them when you need to .. Sorry about the loss of your female .. I did not see how long the tank needs to go fallow for them before adding new/ old ones in or back .. as for the breathing keep the water moving for good 02 exchange and perhaps an air stone also would help .. At this point I am sure there is not much you can do other than wait it out with the outlined treatments given ..
The male is in the display tank and looks perfect. Except for a little nip on the tail fin... No swelling and no white spots. He eats like a horse and swims around everywhere.
At this point should I wait a bit or should I get the meds out of the QT add some live rock and think about getting a new clownfish in there for a week and then put with the male in the display tank?