I like Nitro PDF Professional. It is not free and it does takes a bit of time to feel comfortable with it. They do provide excellent support. Only free for a short period but they are very quick to respond. I have used it to convert Word to PDF. I create the TOC in Word and then create the links in Nitro. I am not an expert on PDF conversion programs but I do believe this one is worth checking out if you don't mind paying for the program.
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