So what would the fix be, aside from setting CSS size to fixed, what am I searching for in the CSS and what do I change it too?

Validate – then use the warnings to know which css file has the problem
break it open and open the css file in a text editor
find:absolute is and change it to position:relative

close it up again (I used ecancrusher to open it and to close it up) validate – Success!

I do like answering my own questions.

Hi All

I too am getting these warnings and indeed setting CSS size to Fixed does cure most of them (one remains) but it does mean the graphics do not resize well. Why can’t we have Indesign outputting clean code ready to use? Imagine if we had to hand recode postscript files everytime we want to send a book to print. ID is partly sold on its ability to create epub files but it still works quite badly compared to how well it outputs for print.

Please don’t make individual pages to send to the printer, one pdf with all the pages in will be far better for the printer – and definitely ask the printer for their preferred settings.
84 pages will probably be fine, if you find it slows down your computer then consider splitting it.

Sounds like you could add hyperlinks to the document, you can set these to go to a page and also set the zoom.
The endnote could have a return link set as a button or piece of text at the end.

Wow indeed – as well as what David has said:
Have you tried outputting to pdfx1a:2001?
It is the pdf setting alot of publishers base their output on.

I have found Readium to be quite good with fixed layout