I'm not a developer but for one of our projects, our customer had over
1,000 PDF files. They were managing this through an access database that
included all the metadata for each file as well as a path to the
location of the physical files on the PC or Server. My developer then
developed an executable via VBScript that extracted that information,
created the folder structure in SharePoint and then imported the file
into the appropriate location. After talking to him, he told me it can
be done via access, excel  or a flat file. You might want to check with
your developer because it can be done.