Yeah, I remember when they started teh 1400 pixel requirement, I was not a happy camper that day...
Amazon doesn't care at all about the data ha! However, their awful pricing rules over shadow their ease of uploading. I still can't believe Apple got in trouble for "price fixing" when Amazon forces us to fit our titles into their "fixed" range, or else we get hit with a massive penalty (loss of royalty, which is the same thing)! That's the one reason I like iTunes over Amazon/Barnes & Noble, though we actually haven't uploaded to B&N yet.
Anyways, my workflow is: InDesign ePub export, Clean it up with Sigil, then use Calibre to split the pages, generate the TOC, and convert to Mobi.
Also, remember ePub is just a Zip file. So if you really want to inspect the file, change it's file extension to .zip and unzip it. I've tried doing this through Finder but it never seems to work so I do it via command line (Terminal). Then I can manually tweak it if needed. One example of this being a requirement, was when I was getting an error from Book Proofer that the ePub was encrypted! Turned out that InDesing placed a little xml file named "encrypted.xml" inside the META-INF folder. Luckily the fix was to just delete the file, zip the data backup and then change the extension back to .epub.