Hmm, well I would just stick with LS, since it is much faster at importing collections from calibre. CM is nice, but chiefly for doing things in bulk from the Kindle UI itself -- oh, and for making things invisible
on fw<5.4.2.
Hyphenation is the one big pain in the neck. The calibre plugin can maybe help. I believe there was also a JBPatch, but it hasn't been updated?
As far as custom margins, it will probably require another patch. Ask in the thread there, kaznelson can probably make one, or help you modify the patches yourself.
Sorry, not a fonts user.