My Shogun responded well to Wal-Mart's Rust Remover, in the auto section with the body repair stuff. It kills the rust, then you can simply clear it with hobby clear if you don't feel like touchup/patching.
Wrenching is fun when you're clueless, better when you're experienced enough to be a danger to yourself and your bikes. It's really a blast when things go like they should, which is sometimes.
The 4 hours today were the best of the holiday season, by far, and there's another frame in the trunk of my car.