i managed to pass epubcheck and flight crew.
the following worked for me:
use mobi, add html files
make a toc using mobi, copy it, convert to utf-8 (be careful), make it valid html, remove old toc and add in new toc.
make a prc
stick prc into calibre, convert to epub, unzip
run kindlegen on content.opf
edit date in content.opf (remove time)
zip it back up and run through epubcheck and flightcrew.