First things first, Download Mepis and boot to it. Once up, log in as root (password is either root or livecd, I forget - it could even be something else). Open qtparted and look at the device name for your Windows drive (something like /dev/hda1), then mount it as such:
mount /dev/hda1 -t ntfs /win
Once mounted, move all of your files to somewhere safe! You should have networking, if you don't, use a flash drive, burn a CD, install another hard drive, whatever - just get your files safe.
Now that your files are secured you can really tear apart your system with no worries. When you performed the in-place upgrade, you were *supposed to* overwrite your Windows system folder (which is what is meant by "in-place", this is NOT where the files you use for school are unless you happen to be learning the internals of Windows. If this is indeed not you, and your school has you placing things in there, you need to find a new school. Anyway, the best recourse (and perhaps the only recourse if XP complains too much) is to reinstall Windows completely, including formatting the hard drive. If you indeed cannot perform a "real" in-place upgrade (choosing your original Windows folder location so as to keep all of your installed applications happy), your best option would be to format the drives as ext3 through Mepis, then run "fsck" on them (just to be sure) and then perform a complete Windows installation, removing the partitions you just made through Mepis.
While this may seem like a lot of work, most of the time will be spent in you waiting for the system to finish doing stuff (transferring files, formatting and checking hard drives and installing the OS). You shouldn't need any other special tools to do this right.
HTH
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