Although Calibre is a great program and is quite powerful it seems like it would be easier to rename all you files and then import them.
I have the equivalent of the program below on my Mac and it is invaluable.
http://www.publicspace.net/windows/B...ame/index.html
I would take all your files and replace the series name with the author in the file name then you can import them and straighten out the series numbering inside calibre.
I found it was easier to get my file names right before importing, rather than the other way around. So, I have many 'droplet' scripts that rename files to the format I use to import them. Some replace underscores with spaces, flip the author and title, flip the authors name, etc.
Cheers
Archon