I can't help with the Kindle side of things.
For integrating with Goodreads, there is a Goodreads metadata source plugin to assign an id and fetch metadata from Goodreads to calibre. There is also the Goodreads Sync plugin that can be used to sync things like the shelve, review and reading status.
Series info can be added by downloading metadata using one or more of the metadata sources. Or if you know what series to use for a set books, you can use the Manage Series plugin to do it.
Can't help with the cover as I take whatever is the best looking cover I see when getting the metadata.
And I also can't help with automating this. I update the metadata as I add a books. That is rarely more than a few a week, so it doesn't take much time. You could try using the bulk metadata download for batches and trust it to get things right. if the titles and authors are correct, this is reasonably accurate, but there can be problems with similar titles.
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