thanks! I've had fair success exporting to .mobi from ID5 using Amazon's plug-in for InDesign. I do a similar workflow to you. Making a copy of the final InDesign file, cleaning it up as necessary, making sure there are few if any manual overrides. Since I create the book in ID5 myself, I began planning ahead for export to epub so this process goes more smoothly. I make another copy of the cleaned up file for export to .mobi, which includes putting an image of the book cover on the very first page, and the back cover on the last page.
The export is fairly clean, but still needs a few tweaks, so I crack open the .mobi with Springy, and edit the files in Dreamweaver using code view, or you can use any html text editor.
A number of people seem to think Word is a better tool, but I think Word sucks. For some people, though, who can't afford a professional book layout tool like InDesign, Word is their only option.
I am confident (well, hopeful at least) that Adobe will hear our cries and make the export process go more smoothly in the future. Come on ID6! But only if they fix the epub export - and the footnote function - it would be nice if that were spiffed up too!