I was in this very same situation yesterday. There's a lot of conflicting documentation out there, and the Ubuntu package for mod_perl2 doesn't make any changes to apache conf, as far as I can tell.

The problem I eventually ran into is that Apache::Registry depends on mod_perl, and doesn't recognize mod_perl2 as fulfilling that dependency (Which, I suppose it doesn't)

Using ModPerl::Registry as your handler and cleaning up your conf, as suggested by asz, should solve your problem.