That tank sounds just superb. I wouldn't worry about the shell rot either, as it's not contagious, but due to poor water quality and lack of good lighting. There's no need to separate them, therefore, providing they're compatible. In the spring buy them a farm pond and give them direct sunlight, which is a sure cure for shell rot. For now, use a betadine solution and dry dock it for hours at a time. Don't pick away its scute either, but use a soft toothbrush to scrub away the fungus.

Good luck.