Your site and Mastodon profile seem to be set up properly.
Did you make sure to add the link on your Mastodon profile after adding the link on your website? According to the official docs (https://docs.joinmastodon.org/user/profile/#verification):
Make sure to save your profile after adding the rel-me link to your web page! The verification process is triggered when you save your profile, and may take some time before completing. If you have added the rel-me link and verification is not working, then try daeleting the link, saving, re-adding the link, and saving again.
Automatic conversion to Kepub is a benefit Calibre has, but the same thing can be done by running Kepubify before copying the files manually.