yup.
When uninstalling, choose to have the registry cleeaned too. You will lose things like custom presets in dialogues such as rename from properties, toolbar customisations, and I'm also pretty sure you'll lose any "sorting" you have saved.
Your data folder will have your library, and most things pertaining to it (album art, thumbnails etc.) but all your options will be reset to default settings.
Tip:
This is why I don't bother installing programs on a different partition to windows. They are so closely tied to the registry, that in this context, they almost become part of the OS.
Next time you're carving up your drives, make the system drive bigger and format it. Install windows and get all your hardware drivers etc. installed and running fine. Configure your hardware the way you like it. Do the same for windows, and hit windows update to get your installation up-to-date.
Next, install and configure your most favourite/essential software and finally, defrag the drive.
When all that's done,
then make your ghost image. You will then have a clean, reasonably up-to-date windows installation, configured the way you like it, with your essential apps pre-installed and configured.
That is a lot of time saved into a ghost image that'll take around 15 minutes to run.
Next, work out a strategy that keeps data backed up on your other drives. track down software such as second copy 2000 or backup plus. I use the first of those to do daily backups of MC's data folder and my "My Documents" folder amongst others. This gives me copys of the data/config files of most used programs/games that are easy to implement to bring the ghost image bang up-to-date after applying it.
end of tip
-marko.