Here are the Prequel Trilogy Library of Congress Records:
1999 - The Phantom Menace
http://lccn.loc.gov/99468631
Acquisition Source: Received: 6/1/1999; viewing print ; copyright deposit--RNR; Copyright Collection.
2002 - Attack of the Clones
http://lccn.loc.gov/2002636427
Acquisition Source: Received: 6-14-2002; viewing print; copyright deposit--RNR; Copyright Collection.
2005 - Revenge of the Sith
http://lccn.loc.gov/2005644161
Acquisition Source: Received: 6/15/2005; viewing print; copyright deposit--RNR; Copyright Collection.
So for TPM and AotC, the variations between the film and digital opening day projections are not archived.
2008 - The Clone Wars
http://lccn.loc.gov/2008636030
Acquisition Source: Received: 2008-09-30; viewing print; copyright deposit; Copyright Collection.
Yeah the LoC archives moved to Y/M/D records.
*Edit*
Can't seem to locate the 2004 & 2006 DVD sets... If you want to give it a shot: http://catalog.loc.gov/