And /usr/local/pgsql was re-initdbed with a 9.0 cluster, because previously it was the 9.3 cluster?
And you are sure /usr/local/bin has the 9.3 binaries?
Personally I would say at this point the relationships between versions are so confused it would seem best to start from scratch.
My suggestions:
1) Create a new jail with a copy of the test 9.0 cluster located in /usr/local/pgsql.
2) In that jail install a new 9.3 cluster using the --prefix= switch to configure to have it install in a different location in the jail.
3) Use pg_upgrade.
Before every test I do a ZFS rollback which resets all data on the disk back to the last snapshot. So essentially every time it's dealing with a new install. However I will give a try your suggestions that you had in your next email (I can see into the future) and report back.
-Thanks