I have found a workaround to the ITMS-9000 problem with the help of deep searching with Ms Google.
I opened my epub in Sigil, I then saved it as a new epub.
I unzipped the epub to have a look and it made some changes. In the ncx it replaced spaces in file names with %20. It also reordered the contents of the epub. So inside there is content.opf, toc.ncx, a text folder, images folder, and styles folder. Whilst Sigil arranges the content of the epub to a different way Im not complaining as I have uploaded it with iTunes Producer and haven't had any error messages from Apple yet
. I hope this helps anybody else who this drives mental.
But if anybody does know how I could have fixed my epub without using Sigil then I'd be happy to know as I tried multiple combinations of using %20 and underscores/ hyphens in the ncx file and renaming the html files and editing the opf file references.
But am happy now.