Nevermind, I found my answer with a google search:
https://www.mobileread.com/forums/sho...d.php?t=129364
and
http://manual.calibre-ebook.com/conv...le-of-contents
and then found the TOC options in Calibre's conversion settings. I must have been looking all over the place except for there (stupid). For some reason the TOC's wouldn't update with the chapters Calibre found (despite the limit being set high enough) -- I had to "Force use of auto-generated TOC."
Glad I have my TOC's now