Question: al-Qaeda or Al-Qaeda?

Note: This inquiry has been divided into two questions. See "Question: Transliterating Arabic" for the answer to the second part.

I'm editing a book for publication in the spring on US torture and empire-building at home and abroad. Two questions about transliterating Arabic have come up, particularly the political connotations of each choice. I would be grateful to any insight you might provide.

First, al-Qaeda translates to English as "the foundation." This is how it appears on the Aljazeera website, for example. However, the New York Times treats it as the name of a formal organization, Al Qaeda. This seems wrong to me. Your thoughts?

Second, and this is painful: At one point the author details a typical "detainee-processing" at Abu Ghraib, which includes a forced rectal exam. This is the only thing that is typically said in Arabic to those captured by the US military: Wa' all'an lill act el amptihan! (trans. And now for the ass inspection!) Naturally, I'm especially concerned about the accuracy of this transliteration, particularly the breaths. Please advise, if you would.