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Hi! Did you ever get anywhere with this? I too am interested in interoperating KOReader / Moon+ / Calibre.
The biggest challenge I see is in reverse engineering the Moon+ annotations format. I went down this road about a year ago and hit a wall pretty quickly. I didn't try reaching out to the developer so I am not sure how forthcoming he is about sharing that stuff.
EDIT: the "3rd tool" you proposed here can probably be covered by adding custom metadata columns in Calibre.
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