Well, if you want ease of copying ebooks, you could always use iBooks. You just add your epub files to iTunes and they'll copy over to iBooks on sync.
No idea why your 3.1 lost network access. Mine works fine. Granted, sometimes, the Bonjour service isn't working so the Calibre library doesn't automatically show up on Stanza. However, I can always access the catalog using a link manually added to Book Sources (e.g.
http://192.168.1.2:8080/stanza).