I don't use Goodreads, but just checked and my non-Amazon books are recognized by Goodreads. I insert the Amazon ASIN number into the book metadata id's field during my conversion flow in Calibre. I configure the metadata editor to only use Amazon as a search site and then I do 'edit metadata> download only metadata and covers' (alternately you could just go to Amazon, find the kindle edition and cut and paste the ASIN #). Then, using the Quality Check plug in for Calibre, I do a 'Fix > Fix ASIN for Kindle Fire'.
There may be alternate methods but this works for me...good luck!
* fyi- this process can be done to multiple books at the same time.
Also, the important step after you place the ASIN # in the id's field is to do the Fix Asin for Kindle fire.( this embeds the info in the proper location )