The sores on the under side sound like where the koi has over wintered and depending on the severity should need no more than topical treatments. Is the sores on the fins like a white lumpy substance as this time of year bacteria in the pond should be at a minimum and there shouldn't be many problems with bacterial infection.

If the fish is gulping at the surface this normally indicates a lack of oxygen in the pond. I would suggest putting more air stones in and saturating the pond with oxygen. As for the "swim bladder infection" tis can normally be sorted by salt.
I would agree that it is best to separate the fish as 1) if there is infection then this could rapidly spread and 2) if makes it far easier to medicate say 1000 gallons than a 3000 gallon pond as you are a) only treating the infected fish b) it is cheaper and c) the medication could knock back your filtration.
This is why I always recommend getting a quarantine tank