Sometimes I make e-books out of printed copies, if a digital version doesn't exist yet on Amazon. I scan the pages, extract text with OCR, then create an e-book by editing CSS style sheets with some tools. Finally, I convert it in an AZW3 format, so that I can add hyphenation with Calibre and send it to my Kindle. The result looks great.
Unfortunately AZW3 files can't be sent to Kindle via e-mail and therefore can't get stored in the Cloud. So there are only 2 options:
Send the AZW3 file via USB cable (and forget about the Cloud storage service)
Send a MOBI file via email (and forget hyphenation, as it is only supported by AZW3 files).
So does anybody know a way to send a hyphenated AZW3 file to the Kindle via email and store it in the Cloud?
Sounds like you can't. I usually just do the second option you listed when I convert a physical book to a digital version. For articles, I usually just create a text file and email it to my Fire table, which also adds it to the cloud.
Edit to add: Have you seen this software? I've bought it when it first came out, but never did much but play around with it.
I think part of the reason for the bad reviews is that it's just not an easy process converting a physical book into a digital one. It takes a lot of work. I do something similar to you, after OCR I use a freeware HTML editor to format the text and then use Calibre to convert to mobi format. Back in the day I had a program that I used to make PDB ebooks for my Palm PDA.