Since you understand editing the registry for a clean boot, your next step is
learning to 'export' the keys that you don't want to load, and creating a
combined ' *.REG ' file to run to undo the entries, reboot, run the game,
then run another reg file to redo the entries.
Open regedt32 and highligh some small subkey, and use the File menu to
'export' it to a reg file. delete the key, then run the reg file. You will
find the key recreated.
Removing a key is a bit more technical. It can be done in a bat file, but
scripting is the best way.
Learn to Script:
http://www.microsoft.com/technet/scriptcenter/learnit.mspx
Run CMD, and from the prompt, type REG /?