Whispersync is by definition not for sideloaded books (in the sense that sideloaded books usually aren't from Amazon. but made/converted yourself). Adding ASIN to the identifiers will not be updated in the book, as Kovid was worried this would lead to confusion.
You can use
Java MOBI Metadata Editor, however, to embed new ASIN's into the correct Meta fields, but it cannot be done in bulk.
As far as getting the Kindle editions, you will have to go to Edit metadata and download the metadata manually, it will give you an option to select which edition to use, if multiple editions are found. This includes choosing between hardcover and Kindle editions.