Is it known who actually wrote Bourbaki's Elements of the History of Mathematics?
Different people wrote different parts. Weil indicates somewhere that he wrote the Note historique about infinitesimal calculus. A perusal of Archives de l'Association des Collaborateurs de Nicolas Bourbaki might provide further hints.
Other possible sources of information are articles and interviews by Henri Cartan, Jean Dieudonné, Armand Borel, and Laurent Schwartz about their involvement with Bourbaki.
Among the living, Pierre Cartier, Roger Godement and Jean-Pierre Serre should be able to provide you ample information. Bourbaki's biographer Liliane Beaulieu might be another source of information.
Addendum (2013/03/31) Bourbaki's editor Hermann has donated all his papers to the Bibliothèque Nationale de France. See their announcement (http://www.datapressepremium.com/RMDIFF/1805134//archivesbourbaki2.pdf) and an article in Libération's science blog (http://sciences.blogs.liberation.fr/home/2012/11/les-archives-bourbaki-%C3%A0-la-bnf.html).