When I got home from work the larger of the sores was more smoothed out, but the smaller sore was protruding more. It doesn't look like fungus. Ulceration maybe?
I've done a 50% water change and took the sick guy out for a salt bath. I added the recommended dose of artemiss to the tank and put the sick fish back into the tank, but in a fry net so I can more easily monitor him. See how we go.