One question out of curiosity. If you remove the books from your Kindle, can you then download books past the point where your downloads stopped? At one time, when I was trying to download a mass of books to my PaperWhite 4, it showed a bunch of downloads as queued and they seemed to be stuck there forever.
With the current tools, you can add the books to calibre from the downloads on your Kindle ereader. The easiest way to do this is to add the books from documents/Downloads\Items01 directory on your Kindle (select the books not the subdirectories). If some of them import as KFX-ZIP, you can try removing the download, re-downloading on your Kindle and then adding them to calibre.
Basically, make sure you have the KFX Input plugin and the latest
autorelease of noDRM's fork of DeDRM before getting started.
Note that unless you have a Colorsoft, any images will be in greyscale and the image size will be limited.