Hopefully you got it fixed...
This may be my lack of knowledge of the Mobipocket format showing, but is there a tool that will just unpack the Mobipocket file? Calibre does some additional processing on the HTML, but I'd rather have it in as raw a format as possible.

(I'm trying to determine which will be better for converting to ePub - Mobipocket or MS Reader. I'm thinking MS Reader, but it's hard to tell for sure when the Mobipocket tools are transformative...)
Mobiunpack - you'll need to install Python to use the script, which you can find here, attached to post 5 and grab the attachment (version 0.17 at last count).

I haven't done much conversion work from unpacked .mobi, but converting unpacked MS Reader to .epub is pretty trivial.
Thanks! That's exactly what I was looking for. And answers my question, to boot (stick to MS Reader - between higher-resolution images and non-proprietary tags, it'll work better for my purposes).
I think there is still a need for a comprehensive tool that can do a few conversions at a time.
Hi!

I know this will be a silly question... but I'm new to Kindle and Mobi having just switched from a Kobo and I need to fix up the table of contents in my Mobi files. How exactly do I use mobi2oeb? I tried using the command after navigating to the sub dir the Mobi is in, but it tells me that the command is not recognized as an internal or external command... i'm doing something wrong aren't i?