How do I create an accessible PDF for Thesaurus with many chapters, from InDesign CS 5.5 and Acrobat

Question

Hi folks,
I have redesigned a Thesaurus (controlled vocabulary for an Agency's archives) in InDesign CS 5.5. I am now preparing an accessible PDF from the many files (using a Book created in InDesign). The front cover, front matter and back cover are not part of the Book, to keep the page numbering simple.
The Book includes two main sections, an Alphabetical display and a Hierarchical display of terms and their relations. I created chapters per alphabet listings, i.e. Alphabetical Display A, B, C, etc. So there are over 50 chapters, including cover, front matter, etc.
I've successfully made the front cover and front matter PDFs after viewing videos here: http://tv.adobe.com/watch/accessibility-adobe/preparing-indesign-files-for-accessibility/ and downloading and using this recommended Action for Acrobat: InDesign CS5_5 Accessibility Touchup.sequ
Several questions specific to this project don't seem to be addressed in the videos, however.
First, I'd like to know if I can create an accessible PDF using the Book function > Export Book to PDF. Or do I need to make a PDF per chapter? The book has over 50 chapters (by alphabet, twice), so creating them one by one will take a lot more time, but I'll do it if that's the best practice.
After creating the PDFs, if I use (in Acrobat): Create > Combine Files into PDF to make one full PDF (over 600 pages BTW), will the final PDF retain accessibility settings? Do I need to run the Accessibility Report again for the combined PDF?
I used InTools.com Power Headers plugin to add a page header that automatically shows the new first term used per page. So, one chapter (with Chapter Title as H1) will have a different page header (which will be H2) per page, however the text flows through the whole chapter. I don't see where to add the page headers to the Article Window in InDesign. Do I add in this order: H1, H2, text (for whole chapter), H2, H2, H2, etc. Will I need to work on the PDF in Acrobat, where pages will be shown, in order to get the correct H2 with the correct text on the page? Am I missing something?
Will I have any issues with Bookmarks that requires a specific workflow?
I think that's about it, though I might run into more questions as I progress through the project.
Thanks, Marilyn

Answer 1

I understand why you need updated running headers in your book. To a sighted reader these serve as a guide to where you are and help you find things quickly.  In addition, if you are exporting your data to XML or HTML from the tagged PDF it would also be important to have these in the proper location. 
But for accessibility purposes, it doesn't have to be there because the screen reader reads everything in linear order, line by line.  No one is looking at the page.  A user listening to the screen reader read the page is going to hear this heading, just before the actual word itself. So they will hear the first word on the page twice.  It's not the end of the world if it's there, but such headings are not necessary for accessibility unless they are not repetitive and contain information that is not otherwise available.
So I would say, fine if you need them or want them there, it's just one word. 
I think you should try exporting your book to PDF (or even just a chapter of the book) and look at the tags panel in Acrobat to see if you are getting the result you want.  I can't tell you exactly what you should do to get those results, you are using a plug-in I don't have. 
I can tell you I didn't have to add the headers to any article at all, they just automatically export if the other articles in the file are added and you don't select the header style option "not for export as XML."
You may not experience the same results with your plug-in, but I think it will probably work the same way. 
Give it a try and best of luck.