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At last I have been able to convert pdfs to mobi/pcr/epub quite satisfactoraly.
As suggested elseware load the pdf into MobiPocket Creator which is free and it will churn out an html and an .pcr. For the table of contents I have found it better to clean out the table in the html and then use the functions in the creator on h1 and h2 etc. to make the table. Also it is posible to put the html into sigil and go straight to epub. There is a tutorial on this subject here.
It takes very little time to do a conversion (Max 1 hr.)
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