Back when I used keyclone, I had a separate wow folder for each toon, but I used a symlink in the 2nd and subsequent wow folders to the "main" wow Data and Interface sub-folders. I don't remember how I set it up though, but it worked like a charm, although I had to take care that I only patched the first wow folder, then I would manually copy the files at the "root" level of the main wow folder to the other folders.