Import Into Windows Mail

In trying to fix up my completely screwed Windows Mail install, I've
tried Exporting, then Reimporting messages. I can't seem to import a
nice, clean copy of the messages and directory structure; it only wants
to import a complete Export. Which has dozens of Recovered folders and
IMHO is severely messed up.

I have successfully been able to simply drag the EML files to a WM
folder. If I create all new folders, then manually drag the 25,000
emails from the appropriate folder, will WM reconstruct things properly?
Will this get rid of the Recovered folders (if I also delete them), or
will it put this all into NEW recovered folders.

Basically, can anyone just help me RECREATE my Windows Mail messages, in
a logical and orderly way (the way I have them visually in WM), and not
rely on Restored folders and the complete MESS they provide??

Regards,

Rick Raisley