Personally, I think you'd be better off using
Mobiunpack to extract the HTML (it preserves the original formatting along with any opf and ncx info for chapter marks and start points and such), editing the opf to add in your cover image, and generating a new Mobi via KindleGen or similar. It takes only a couple of minutes and I find it's much simpler that way.
Mind you, there might be an easier way to do it via Calibre, though perhaps you'd get a better response asking in that forum.