I was going to suggest Calibre, but see you have already tried that. As you’ve found, PDF’s are tricky to convert and it’s virtually impossible to get a linked TOC. There are two possible solutions. First, you can visit mobileread.com; they have discussion forums with technical advice about using Calibre. Second, have you tried to find the book online in ebook format? If the book is in the public domain, you can probably find it at feedbooks.com (and as a bonus, their books usually feature a linked TOC).