It's hard to understand what's going on. You've typed a lot, but I'm not super clear about the details. So here are a few things:
If you have an MC library that has these files in it already, you can backup that library (the metadata from the database) and restore it into your new MC library that you are creating now: File > Library > Backup library (on old MC installation). File > Library > Restore library (on new MC installation).
If your files won't import with Tools > Import > Import a folder, then something is probably wrong with your files. There's also a possibility that you're using a rare file format and MC doesn't full support it. I seem to recall some compatibility issue with 32 bit WAV files from a while back. Those are very unusual and entirely unnecessary. But some people use them.
If you can provide more details about your failures, maybe we can help. Any error messages, dialog boxes, etc, would be helpful. Alternatively, you could enable logging, do your import, wait for the failures, then do "submit log" to create a zip file of the log. Then attach it here for analysis.
http://wiki.jriver.com/index.php/LoggingEDIT: Re-reading your post, I'm wondering if you just have a library that was previously used and has old entries for your files, which is keeping them from being re-imported. Try one of these two procedures:
A. Build a brand new library and import into that: File > Library > Library Manager > Add Library .
OR
B. Entirely clear your existing library. This will reset everything. All of your imported media will be removed from the Library, but will remain in place on disk. File > Library > Clear Library .
Then try to import your music folder again.
Good luck.
Brian.