For those of you keeping track, I restored a database backup, and I was still experiencing the same problem. So I then set CheckValidity=true to run the installer again. I ran the installer, told the database section to 'leave data and add new' and pointed the siteaccess to my sitedesign.
So far this has restored functionality. What I will now do is monitor closely my changes to see what causes it to break again.
Edit: I have now loaded all my correct templates and default index page. So far everything is working with my custom classes, except now I am getting a strange node_id error which I have posted about here: http://ez.no/community/forum/setup_design/node_id_is_empty