I just hope you're trying this on a test setup. Or have good backups ...
The "uid" and "owner_id" fields in every story hold the author's user id. So of course, when on site #1 user #42 is Frank and on site #2 it's Tom, you get a mix-up. And there are more tables that depend on that uid, like the user's settings, permissions, comments, stuff in plugins, etc. etc.
In other words: It's not nearly as easy as you think. And requires a lot of advance planning and a good idea of what you are doing ...
bye, Dirk