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I would try to use Sigil for what you're trying and convert to ePub. Then I would use Calibre to convert to mobi format for your Kindle.
However, Mobipocket Creator would also be good for this.
If you're having trouble with one, you'll possibly have a problem with the other. I tend to use search and replace based on regular expressions to add styles directly in HTML so that I can then use the automated functions to build table of contents and split chapters into separate files etc...
If this is exactly the kind of thing you're not comfortable with, then maybe my advice isn't worth much.
However, thanks for the recommendation on Nuance's PDF Converter Professional 7. If I could find a professional version of something I could absolutely rely on to convert from PDF to another format I'd probably give it a go.
Regards
Caleb
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