Originally Posted by Tugger
1. Start with my .mobi from the InDesign plugin
It might be easier if you generated .ePubs with InDesign. KindleGen can compile them and if you rename them to .zip, you can navigate them with Windows Explorer and replace files. (Don't unzip them, though.)
Exporting ePubs might also solve your unspecified font problem, and, depending on the InDesign version that you have, you might even be able to define the Go to Beginning anchor and the corresponding guide item directly in InDesign.