[kovidgoyal]

Use mobi2mobi and there is a wiki page that documents the MOBI header in the mobileread wiki. And of course there is the calibre source code. Look in the ebooks/mobi/*.py files.

You can dump a mobi's headers (and all records) in a nice text representation on which you can run diff by

calibre-debug --inspect-mobi filename.mobi

Compare a kindlegen mobi to a calibre mobi and see if you can spot the difference. If you find something that look suspicious either zero it out in the kindlegen mobi or change it in the calibre mobi (the latter is much harder if it involves adding fields)

But be warned, the MOBI format was designed by a bunch of monkeys on a sugar high.