Random thought: if you are willing to take out the SD card and put into the card reader *once* then you can do the initial transfer of all your books more more quickly. Mount the SD card in the card reader then copy your entire calibre library to the card. Be sure that the metadata.db file is copied. It wouldn't be silly to try to open the copied library with calibre just to be sure.
Next, put the SD card back into your device and open it with CC's "Local library" cloud connection. You can then transfer books at SD card speed, which (I think) will be around 1/3 to 1/2 second per book, the time it takes CC to update its database.
Another random thought: try using the content server connection. It uses the network quite differently than the wireless device connection, which might result in better performance.
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