I'm no guru either, but I do note that I cannot see why these errors would be caused by chapter header changes in sigil. They seem to indicate, for the most part, that something is missing from the epub package. You can (as you may know) open the epub as a zip file (rename *.epub to *.zip if necessary) and verify whether the indicated resource (namely the cover image in most cases) is really present where it says it is.
re: File number 3, with all the "attribute "clear" not allowed at this point; ignored" errors. These errors are probably not the reason why it won't open on your reader. I think the real problem is the first error listed: "unfinished element".
How did you generate these epubs in the first place? Or did you download them from somewhere else?
In any case, I'm getting the sense that it is not anything YOU or Sigil did wrong that is causing this. Some deeper magic must be at work. Not that I'm quite ready to absolve "tidy" just yet.
Oh, and BTW what version of sigil are you using? Hopefully the most recent, 0.2.3