OK, so I worked out which files to edit and I actually managed to change the Apache/WebDAV ports on a clean 10.8 Server.
By clean I mean I installed 10.8.0, updated to 10.8.3 via the combo updater, then installed the latest version of Server app and configured the services.
Having done that I was able to make the required changes and all is working well. I then replicated the process on my live server but it throws up an error when I try to start up the WebDAV sharing.
This thread outlines the same issue:
https://discussions.apple.com/thread/4199421?start=0&tstart=0
I am getting this exact problem, in that any manual change at all to the 0000_any_443_.conf file will cause WebDAV to fail to start. This is annoying because I need to change that file. Its also annoying because the problem isnt there on my 'clean' server.
I deleted the entire /Library/Server/ folder and the Server.app and reinstalled Server.app from the App Store, recreating the /Library/Server folder from scratch. This cleared out the apache config files which I tried to re-modify, but all the file sharing settings were retained. Does anyone think it would be worth deleting all the sharepoints? Any other ideas?