It may be some consolation, that the same errors may be repeated in each section. If you can search and replace a problem for one, it may clear up the same one in the other sections.
You do know that epubs are all just .zip files collected together. You can unzip the file and open a section in a text editor to see if you can figure out what is going wrong. Tweak epub, part of calibre or as a separate program would speed up the opening process, if seeing the html is helpful to you.
The messages from Flight Crew can be less than helpful. The width message can sometimes mean that you have width specified in one place in the table and nowhere else! So just use them as a pointer for something that might be out of place.