I prefer the 2003 model. It has a better aerodynamic fork than the 06. And I hate the Alpha Q fork. Tyler Hamilton won LBL on the 2003 model.
Mine built up with Ksyrium SL's, all Dura Ace, 51 cm, Less 199 bars - weighs 17.4 lbs. It's my fastest bike and I hit 32.9 mph on it (flats no wind).
Show us a pic of your built bike!