Blast. Just when I was reaching around to pat myself on the back for, I notice some big problems.
First, the home page is all messed up with duplicates of many things. Doesn't seem to happen on the local version, which means it is going to be tricky as all get out to solve.
Secondly, the markup on the Mothership leaves a lot to be desired. That one will be a lot easier.
There are probably others too.