The pdf you posted shows your many-boxes TOC page to be a thing of beauty, and I'm sure you spent many hours making it so.
Here's the thing...shrink it down to a 3.5 inch wide Kindle screen, or even a 4.625 inch Kobo Forma screen. (And think smart phone?!) How many people could even read it at that size? So even if you get a perfect page-to-page conversion, will it really do any good for e-reading devices? Larger tablets, maybe...but they are OK reading the pdf anyway.
When I started messing with ebooks I spent untold hours trying to get fancy stuff readable on my Kindle, with a huge lack of success. Now the fact of tiny real estate and readability comes first, fancy last; that's my (grudging) reality.
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