I'd recommend Sigil, so long as you keep things simple, the epubs will convert very well to mobi.
The process really isn't all that time consuming after you've done it once - and for the most part isn't necessary at all. You just need to get the PDF converted to html then add it to a blank book and you'll be on your way. If the converted html has preserved the italics, bolding and important indents (i.e., written letters), you should be able to ignore pretty much everything else and just mark up the chapter (i.e., make them headings) and generate the ToC. Calibre can throw in the metadata and cover etc if you do an epub->epub conversion afterwards if you're lazy
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