Creating 508 Adobe Acrobat Accessible Docs from various sources and formats

Question

Note: I have no 508 training, except for perusing of documents on the web.
I need to create searchable 508 Compliance report documents for Adobe Acrobat (not for the web at this time) from merged PDF files. 
To create these reports, I do not have originals, all I have been given are PDFs, some of which have been created from Word and others scanned (some with OCR and some not).  Some of the reports are converted directly from Word but may also be a combination of electronic and scanned pages (signature pages, graphics, appendices, etc.)  Often the scanned pages have not been scanned to actual letter size (8.5 x. 11), but are smaller.  Sometimes they are larger or A4.
In preparing the final report, I take all of the PDFs and merge them into one document.
I add watermarks and headers/footers to the whole document. 
In order to get all of the watermarks and headers/footers to align on the page with ease, I need all of the pages to be the standard letter size of 8.5 x 11 without losing any information.
The only way I can figure out how to achieve this is to take the pages (usually scanned pages) that need to be enlarged (sometimes reduced) and Print to a PDF. 
This will create a new PDF of the existing PDF; making it the standard letter size of 8.5 x 11, without cropping.
I can then replace the odd-sized pages with the new PDF pages, creating a document where all of the pages are now the standard letter size of 8.5 x 11.
Once my document is all the same size, I can add my watermarks and header/footers.
I still need to make the whole document a searchable 508 Adobe Acrobat compliant document.
I believe I need to run the OCR Text Recognition to convert/capture scanned pages and pictures to make this document a searchable 508 Adobe Acrobat compliant document.
I tried running the OCR text recognition on the current merged (160 pages) PDF document (before adding my watermarks, headers/footers) to capture the scanned text, and I receive the following errors:
        This page contains renderable text.
        This page has graphics other than images or text on it. It cannot be captured.
When I ran the Adobe Acrobat Accessibility checker, I get the following errors:
       The first page is a scanned signature page: the error says
1 image with no alternate text
            1 element(s) that are not contained within the structure tree.
1.     Inaccessible page content
     Most of the remaining detailed report errors are:
Inaccessible page content
1 element(s) that are not contained within the structure tree.
I tested one page and used the Touch Up Reading Order tool and added alternate text to a signature block, ran the accessibility checker again, but still came back with alternate text errors.
I am open to suggestions.  Feel free to advise me from beginning to end in regards to what I’m trying to accomplish. 
THANK YOU!

Answer 1

You do have a boat load of work.
     This page contains renderable text.
     This page has graphics other than images or text on it. It cannot be captured.
This isn't an "error". Acrobat's OCR cannot process  PDF page content that is not exclusively an image.
    1 image with no alternate text
When properly tagged, an image or graphic in a PDF is identified by the PDF element "Figure"
(<Figure>).
All Figures shall have an Alternate Text Description.
You may have images/graphics that are tagged as Figures but should be Artifacts.
OCR - The hidden layer of OCR output provided by Searchable Image or Searchable Image (Exact)
is, for practicable purposes, not something one can effectively created Tagged PDF from.
Prior to Acrobat 9 one would use Formatted Text and Graphics. With Acrobat 9 one would use
ClearScan. Alternatively, one might just re-key the content in an authoring application and output Tagged, accessible PDF.
Watermarks & Header/Footers -
Oh boy; well, once you have everything else in a "green board" line up you'd add these and manually
"fold" them into the structure tree via proper tagging.
So, the first step is to gain at least a fundamental understanding of what an Accessible PDF is and
how to create it. Then you'd want to become familiar with Section 508 1194.22.
As each of the paragraphs are correlated to WCAG 1.0, you'll want to review it to understand what
the correlation is and how it relates to PDF.
However, Section 508 will be changing.
The Draft Updated Standards and Guidelines are on the street.
The window for public comment closed a few weeks ago.
PDF - What it is: An ISO Standard (ISO 32000-1:2008)
Obtain a free version of this ISO Standard to study what "Tagged" PDF is (Accessibiity is just one facility associated with Tagged PDF).
http://www.acrobatusers.com/blogs/leonardr/adobe-posts-free-iso-32000
Section 508, 1194.22
http://www.section508.gov/index.cfm?FuseAction=Content&ID=12#Web
The "change" that is pending - at the Access Board's site:
Section 508 Homepage: Electronic and Information Technology
http://www.access-board.gov/508.htm
Download the PDF of the Draft Updated Standards and Guidelines for review and study.
Note that, in part, this more closely aligns Section 508 to WCAG 2.0.
WCAG 1.0
http://www.w3.org/TR/1999/WAI-WEBCONTENT-19990505/
WCAG 2.0
http://www.w3.org/WAI/intro/wcag.php
Start with the Overview and work through the technical, educational, and transition to 2.0 information.
"How To"
Still relevant in an Acrobat 9 world:
Creating Accessible PDFs using Adobe Acrobat 7.0 Professional, Greg Pisocky
http://www.appligent.com/adobeaccessibility
(Download to PDF file and exercise files (ZIP file).
For Acrobat 9:
http://www.adobe.com/accessibility/products/acrobat/
For links to an accessibility overview and FAQ.
Acrobat accessibility training resources
http://www.adobe.com/accessibility/products/acrobat/training.html
Yes, review - study all.
A resource listing at Acrobat Users Community
(PDF Tags Books thread)
http://www.acrobatusers.com/forums/aucbb/viewtopic.php?id=15622
I've not checked all the links recently - some destinations of the URLs may be gone
(floatsom on in the deep blue of the web <g>).
Regardless, much "how to" was in PDF documents Adobe published for earlier Acrobat releases.
It is still relevant.
Accessibility on demand eSeminars:
http://www.acrobatusers.com/learning_center/eseminars/on_demand
Scroll through the pages of links to the recorded eSeminars to locate and view -
--| David Mankin's "Scanning and OCR"
--| Duff Johnson's "Tech Talk: Making PDF files comply with Section 508"
Transcript, PDF of PowerPoint file, other information for download at Lori Kassuba's AUC Blog -
http://www.acrobatusers.com/blogs/lkassuba/making-pdfs-comply-section-508-tech-talk-0
--| Charlie Pike's "Accessibility"
"Q&A" transcript at Lori Kassuba's AUC Blog -
http://www.acrobatusers.com/blogs/lkassuba/top-questions-june-accessibility-eseminar
Accessibility Forum at AUC - Accessible PDF related posts
http://www.acrobatusers.com/forums/aucbb/viewforum.php?id=18
Read through Duff Johnson's AUC Blog and Talking PDF articles related to accessible PDF.
--| AUC Blog  http://www.acrobatusers.com/blogs/duffjohnson
--| "Talking PDF" http://www.appligent.com/talkingpdf
Visit Adobe TV
--| Ensuring Your PDF is Accessible
http://tv.adobe.com/watch/acrobat-tips-and-tricks/ensuring-your-pdf-is-accessible/
--| Navigating an Accessible PDF Document (Part 1)
http://tv.adobe.com/watch/acrobat-tips-and-tricks/navigating-an-accessible-pdf-document-pa rt-1/
--| Navigating an Accessible PDF Document (Part 2)
http://tv.adobe.com/watch/acrobat-tips-and-tricks/navigating-an-accessible-pdf-document-pa rt-2/
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