UK native, not a teacher.
To stop [somebody] dead means that something has suddenly taken all somebody's attention, in this case, the author means that whilst he was considering the wider context, suddenly he became very aware of the subtleties, to the exclusion of everything else. This is a way of expressing his surprise at the importance of the small things. There is another phrase, similar in meaning, that reads "to stop [somebody] hin his tracks". This tends to mean that something can be suddenly stopped, but is less likely to be used with 'for a moment', and is more likely to infer that something can quickly be stopped but will not resume, e.g "Clearasil stops acne in its tracks", "New regulations stop cowboy builders in their tracks".
Hope that helps.