"Well, sure - are they? Do the referenced files exist at the specified locations?"
AND:
"Your configuration sounds unusual (to say the least), and it's a little hard to fill in the blanks. Maybe if you could explain how you expected the disk to be restructured, it might be possible to determine what's gone wrong."
Yeah, I was going to suggest running EDIT to look at your msdos.sys and config.sys as jboy outlined above (c:\windows\command\edit c:\config.sys), but if these programs/directories/files have been "moved" by P.M., the paths to same probably won't match anymore.
Just to clarify, I gather you're not getting into windows now, correct?
If you can explain how the disk has been restructured it would help a lot. If it helps, I can provide you with an old DOS 16 bit program that will find files under DOS 7.1.