If your folder hierarchy is that well structured throughout, you should be able to let Calibre do most of the dirty work. You can use regular expressions in the adding books- section of the preferences to describe how calibre should interpret the books filename to extract metadata (remember to tick the box that sets metadata to be read from the filename). If you don't know regular expressions, here's a tutorial
A few caveats apply:
This way, you lose every metadata that might be in those books- at least LIT and PDF can contain metadata in themselves.
It might be more sensible to add the non-series books and the series books apart from each other.
You mentioned one book in DOC format. Be aware that Calibre doesn't support that format- you need to convert to RTF, for example. You can do that after the fact, as well, if you just search for DOC format within Calibre, export to disk, convert, then re-import and merge.