I don't really know this stuff, but I'd interepret the report as saying "I've checked everything a computer can check. The remaining points require manual checking of every document." For example 1.3.3 requires that you don't convey information solely with a graphic. A computer can't know whether the text accompanying a graphic is useful, so a person has to do that. On the other hand 4.1.1 refers to something a computer could check, so I may be completely wrong.
"I've been instructed to use the WC3 Web Content Accessibility Guidelines 2.0."
--| The current Section 508 Standard that is applicable here is Subpart B -- Technical Standards, 1194.22, Web-based intranet and internet information and applications.
The Note to 1194.22 identifies that 1194.22's paragraphs (a) through (k) correlate to priority 1 Checkpoints of WCAG 1.0.
WCAG 2.0, in context of the current Section 508 (the "refresh" has not passed through to a Final Rule and is therefore "what might be" rather than "what is"), is not applicable.
The current Section 508 does not incorporate or reference or rely on WCAG 2.0.
--| Do not use "W3C Web Content Accessibility Guidelines 2.0 (Working Draft 27 April 2006)
Any output from this is meaningless.
The "Working Draft" of 2006 does not come close to the actual WCAG 2.0 guidelines (effective late 2008).
A "side by side" comparison readily demonstrates this.
--| While WCAG 2.0 is the "go to" for "web content" (HTML and such) non-WEB content/technology calls for something else.
For PDF this is, specifically, ISO 14289-1:2012. This is the ISO standard for PDF/UA (PDF/UA-1).
--| Useful as well is the ISO standard for PDF (ISO 32000).
A free, ISO authorized, copy is provided by Adobe.
Note that ISO 32000-1 (a standard rather than a recommendation) provides detailed discussion of what Tagged PDF is comprised of.
(Start with section 14.8.)
The ISO standard was released mid-year 2008. WCAG 2.0 was released late 2008.
Consequently there's no objective rational to rely upon a generic (web-centric) recommendation that came after the specific, normative standard (ISO 32000-1) for PDF (a non-web technology).
--| In conjunction with the ISO standards the Achieving WCAG 2.0 with PDF/UA documentation is the definitive "mapping" of accessible PDF (PDF/UA) to WCAG 2.0.
As noted a PDF, intended to be accessible, that does not comply with PDF/UA-1 is, effectively non-WCAG 2.0 compliant.
Unfortunately you're trying to drive the square peg (WCAG 2.0) into the round hole (accessible PDF).
The "round peg" is the alloy of the two ISO standards (32000 and 14289), the "mapping" documentation and the (pending) Implementer's Guidance for ISO 14289.
(PDF/UA Technical Implementation Guide and PDF/UA Technical Implementation Guide for ISO 32000-1)
--| "Validation" tools for accessible PDF (well-formed Tagged PDF)
Currently there is no tool that completely removes the need for the "knowledgeable warm body" for assessing the tagged PDF.
The best workflow for minimal post-processing inspection is proper up front content authoring.
CommonLook Office and MS Word 2010 provide good "author coaching".
The PDF Association is actively working a developing a validation tool for PDF/UA PDF.
--| Your end-users
Typically the end-users of accessible PDF will be using Assistive Tecnology (AT).
Currently, the developers of NVDA are working to provide an AT that is PDF/UA (ISO 14289-1) "aware".
Similarly the Australian government is supporting addressing how PDF/UA compliant PDF delivers on PDF that is accessible.
--| Your documents
Are you working with PDFs that you must process for remediation?
Or, are you working with source, authoring files?
If the later, what would the authoring application(s) be?
--| What's the goal/mission?
If it is accessible PDF then the correct "metrics" are needed.
These are the relevant ISO Standards.
Message was edited by: CtDave
Good to have references if processing PDF to be accessible (well-formed Tagged PDF):
ISO 3200-1 (the PDF standard)
Adobe provides a free, ISO approved, copy.
ISO 3200-2 (when published)
ISO 14289-1 (PDF/UA)
PDF/UA ancilliary reference documentation
--| Achieving WCAG 2.0 with PDF/UA
--| PDF/UA Technical Implementation Guide
--| PDF/UA Technical Implementation Guide for ISO 32000-1