I don't know if this will help but I will add my two cents to this conversation given I was able to sync non-Amazon books between my Kindle, iPad2 and iPhone4.
There was a major thread sometime back and Sadievan along with others helped me figure this out. Let me say upfront that I don't have Kindle Fire but maybe the basic principle of how to do this MAY work with the Fire.
The first key to the process is the ASIN. This makes your devices think your non-Amazon book is in fact a Amazon book. Calibre is the only tool I use to secure the ASIN. I import my non-Amazon books into Calibre and even if they are already mobi, I do another conversion to ensure the ASIN is populated. I have never used the mobi2mobi gui method as it was a little to complicated for me to understand. Calibre after one of its upgrades included the functionality to provide an ASIN on a book which alleviated the need to use the mobi2mobi gui method.
The next step in this process was to place the books in the right folder on the iPad to facilitate the syncing process. As it turned out it is NOT in the Kindle for iPad app. Using a tool called Disk Aid - this allows me to see the root of my iPad or iPhone. After plugging the iPad or iPhone into my Computer, DiskAid accesses my root directory. Once there I go to KindleApp\Library\ebooks folder. I drop the book(s) into this folder, disconnect and voila - I am able to read the book on the iPad/iPhone and when I switch over to my Kindle I am able to go to the last page read.
Again, I don't know how to get to the root directory on the Fire so it will be finding out how to (1)access the root directory and (2)finding the appropriate folder to drop the non-Amazon books into.
These are the steps I used for the iPad/iPhone but my thought is that the general principle may be the same for the Fire, good luck.
P.S. I believe (not sure) that DiskAid is only for Apple products but I imagine there must be another DiskAid "like" tool that will allow you to access the Fire's root directory.
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