I have posted the work in progress notes I have been making while I figure out how to sucessfully upgrade OpenACS.org from a mix of 4.5 and 4.6 to 4.6.3.
It might give some insight into upgrading a site with custom code.
The blog for tracking OpenACS.org upgrade it http://angora.furfly.net:8000. If you want to help get it upgraded, please read the blog and help with questions/errors you see there. If you would like access to the box itself to work directly, let me or dave or somebody know.