I just tried using the KindleUnpack plugin on the book I just finished cleaning up, and it turned out perfectly... no oddball splitting of pages at all, and the rest of the book also turned out better with proper indents and spacing.
I wish I had posted before I finished the current book!

Thank you again for the tips.
Edit: And I noticed the 2 additional posts after I posted. I'll double check my Calibre settings as suggested.