So, I gave all my posts real titles (titles in the Atom feed had been the first 20 characters of a post). Not sure if that's what did it, but Blog Lines now recognizes my blog just fine. The RSS portlet panel extension has bugs that someone has posted fixes for. The My Yahoo RSS portlet never claimed to support Atom feeds anyhow.
The strange thing is that the feed still doesn't validate. So I'll check on that. Maybe look for another site that attempts to validate an Atom feed. But I guess my problems are mostly resolved, for now.