Well, first of all, I'd lose the PDF unless you're building a fixed-format book with all its limitations. Do you have a Word or OpenOffice Writer document? That would be a good start. Look at the fourth post on my blog
notjohnkdp.blogspot.com for the pointers I have collected over the years on that subject.
I think you're on the right track with Sigil, but it does have a learning curve. It's not as easy as throwing a Word doc at the KDP platform and expecting it to fall off as a fully functioning e-book.
There are two TOCs in an e-book. First is the actual (html) TOC at the front of the book. Sigil will build that for you, though personally I don't like the appearance so I build my own. Second is the virtual (NCX) TOC that can be called up as a sidebar on most newer Kindles, Fire tablets, and (I think) Kindle apps. Sigil actually generates that on the fly, from your H1 (H2, H3, H4) headings. All I generally do, toward the end of the process and after I've made any changes in the headings that I'm likely to do, I just go to Tools > Table of Contents > Generate Table of Contents. I glance down the list to make sure it's what I want. I click on OK, and the job is done. Sigil is the best thing that ever happened to self-publishers.
I just upload that epub to the KDP and let it convert there. I hasten to add that I don't do fancy stuff. No drop caps, no media calls, no embedded fonts (and no fixed format). Simple is good.