I edited xorg.conf and changed the modeline to fit my screen.
I've also changed '/usr/pluto/bin/Xconfigure.sh' so it will do nothing.
I've set LinuxMCE to load on startup. When it loads the resolution is as it was before I've touched
xorg.conf. Now, If I kill the X session and start it again ('startx') KDE loads in the resolution I've set.
The nVidia driver does not use modelines - they will be ignored, and only the name of the mode will be used.
Make some changes to your xorg.conf:
In your TVStandard option, change it from 720p to HD720p.
Turn EDID on, as you seem to be using the DVI connector, and the TV will tell the video card all the modes it supports and also which one it prefers.
In you Monitor section, add a DisplaySize option. It won't make any visible difference, but it will help select the correct aspect ratio when you are watching video and TV. See http://www.pillayfamily.com/blogs/index.php/LinuxMCE/2008/02/05/full_screen_tv
for more info.
Once you've fully started up with that configuration, read the contents of /var/log/xorg.0.log and see what the TV is reporting back, and you will be able to figure out what other changes you need to make in your xorg.conf.
Finally, once your xorg.conf is set up correctly, copy it over the Pluto version, also in /etc/X11. Whenever you run the AVWizard, the first thing it does is copy this file over xorg.conf, so you will end up losing your changes.
ColinJones will probably be able to give you a lot of help with this issue, as he has gone through a fair amount of pain and has probably learnt a few tricks along the way.