The Codex plugins need to be updated to work correctly on OS X Lion - on Lion the system identifies files with an epub extension as "org.idpf.epub-container", and unless plugins use the same type they won't work.
Codex uses "com.audacious-software.codex.epub" instead, so will not work on Lion. Have you asked the Codex author to update them?
NB the author of the Lion-friendly Quicklook plugin mentioned earlier in the thread is adding a Spotlight importer. It isn't ready yet, but it is worth keeping an eye on his github page.