So after all this was just mdadm bug #583917 combined with the fact that you used to wrong name (compared to /etc/cryptsetup) when unlocking the crypto device manually. This of course caused the cryptsetup initramfs hook to break when recreating the initramfs. As a consequence, your cryptroot didn't get unlocked during early boot stage. Correct?
Best regards
Alexander Kurtz
PS: You should revert /etc/cryptab to the state it had before all the
debugging (i.e. with "UUID="). You should also revert the change you
made to the cryptsetup initramfs hook, for example like this:
apt-get --reinstall install cryptsetup
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