I'm trying to filter the user stories on my board by Owner, but it returns all user stories I own, plus those owned by others where I may own some tasks. Any way to limit the filter to just the stories I own?
The way that the filter by owner is designed, it will filter on anything that you own, regardless of type. It's meant to give the user an easy way to find any work that pertains to them. So in this case, it may show stories even though you only own the task, not the story.
I'm not sure which board you're using, but if you're using your own Kanban board, you can edit the query on the backend of the app. You might not want to do this if you are sharing the same Custom Page with a team, as it would edit the settings for everyone! You can always create your own custom page with a Kanban Board app on it, though.
Anyway ... just hit the gear icon at the top-right of the app and go to Settings. Then, down in the query field, enter your query -- something like (Owner = "email@example.com")
This should filter only on the type of work item that the board is set to display, and should filter for just those stories you want.
Hope that helps.