So, I changed back to 2.0 by the method I proposed. These are the errors I received and how I solved them. If anyone could give an opinion on how ill advised my solutions are, that would be much appreciated. After I made these changes there were no errors detected.
All of the errors were in OEBPS/content.opf
Code:
ERROR: The "prefix" attribute is not an allowed attribute of the <package> element.
LINE: <package xmlns="http://www.idpf.org/2007/opf" prefix="ibooks: http://vocabulary.itunes.apple.com/rdf/ibooks/vocabulary-extensions-1.0/" unique-identifier="bookid" version="2.0">
sOLUTION: DELETED prefix="ibooks: http://vocabulary.itunes.apple.com/rdf/ibooks/vocabulary-extensions-1.0/"
ERROR: The "property" attribute is not an allowed attribute of the <meta> element.
ERROR:The required attribute "content" is missing from the <meta> element.
ERROR: The required attribute "name" is missing from the <meta> element.
LINE: <meta property="ibooks:specified-fonts">true</meta>
sOLUTION: DELETED WHOLE LINE <meta property="ibooks:specified-fonts">true</meta>
ERROR: The "property" attribute is not an allowed attribute of the <meta> element.
ERROR: The required attribute "content" is missing from the <meta> element.
ERROR: The required attribute "name" is missing from the <meta> element.
LINE: <meta property="dcterms:modified">2016-05-14T18:21:09Z</meta>
sOLUTION: DELETED WHOLE LINE <meta property="dcterms:modified">2016-05-14T18:21:09Z</meta>
I also uploaded it to KDP and it was accepted.