I've made several changes so most of the errors are eliminated.
The only thing left now is:
"Mimetype entry must not have an extra field in its ZIP header"
The content is correct, and the mimetype files is stored uncompressed.
This is created through the zip command, with the mimetype added with 0 compression and then the rest added with compression.
There is another thread about this exact error on this forum, and it is unresolved there, so I'm willing to chalk it up to a problem with the epub checker for now.
I haven't added in the style sheet in yet, I've asked for it to be redownloaded and checked again.
If the paragraphs are still missing, I'll add the stylesheet in.
If it STILL fails, I'll be back
Thanks for your pointers guys!