Alright, so I downloaded the latest update for my Kobo Aura HD (Firmware V4.610075). When I checked this update it had fixed the problem mentioned earlier about positioning. It almost instantly updated the book when I added 4 chapters to a previous upload.
What it did not do was update the ToC. It left it to what the original uploaded ToC was. I'm not sure why that happened, but after switching books back and forth, it still had not updated.
I still personally like my kindle. Some of that is because of how I hold my device and the fact that I can view my kindle on landscape - NOT an option on the Kobo. I tend to read in Landscape for several reasons, though all the time.
Anyway, sorry I didn't get back sooner I forgot about it when I traveled home last week. I don't know if it's still helpful, but it is something that I've put on there for future reference for anyone that may want to know.
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