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I've read through the Non-Disclosure Agreement, and related material. The latest word for the current Beta Phase from SE is:
"Under the FINAL FANTASY XIV: A Realm Reborn Beta Test Agreement, we asked you to keep confidential the features, information, and bugs related to the Beta Test as well as information shared on the Beta Tester Forum. As of June 13, 2013, we grant you permission to disclose information regarding the Beta Test."
Therefore, I do not see any reason why the Instruction Manual for the current phase cannot be posted.
This is in no way an intentional violation of the NDA, and if it becomes apparent that this is indeed a problem, then this post will be removed.
Here is the link to the manual. It was taken from the forum posts, and I think the formatting got a little wonky making it a pdf, but it's good enough. It's 14mb.