Hi Thomas, I agree with Koiszar about hikui, and I first though that the cyst-like lesion were virus infections.
But virus infection that gives such problems can be the Pox virus (only in cold water) and KHV so if you don't have mortality, forget about them.
The epistylis couls be an explanation, so best thing to do would be to look under a microscope. Epistyllis are often carried by trichodina, so if you see some trichodina, the epistylis wont be very far..
If you don'y have any idea of how they look like, just tape the name on google, you'll have a lot of picture and they look both really nice.
If you don't have any microscope, ask your local koïdealer.
I would use some salt to help the osmosis exange and maybe some propolis on the skin if you can clean the skin after after using some anesthetic.
Using salt you'll also treat most of the trichodina (if you have some) but for treating epistylis you will nead higher concentration.
Anyway if you find epistylis, that means that you have a big problem with your water quality.
Let us know...
Marco