Also, when a Special Exempt (SE) is granted (for example when Isner reached the semis of Washington he was given an SE into Montreal because he was unable to play qualifying) is the last direct acceptance just taken out of the tournament? This seems a bit rough on the last direct acceptance but I can't see any other way it could be done.
From the ATP rules - VII.D.4)
4) If the main draw is to be made before a potential special exempt player plays on Friday, then such place(s) shall be drawn in the same manner as qualifier, i.e., four qualifiers ("Q") and one or two "SE" depending on whether there are one or two possibilities. Each of the five or six slots are marked "Q/SE." As soon as the "SE" match results are known, either the "SE" or the next direct acceptance (if the SE lost) is randomly drawn and inserted into the draw.
Edit: Obviously you saw this before I posted