Anyone connected with the 2004 team has a lifetime of admiration from me, but had it not been for the 2006 embarrassment engineered by a bungling FO that was more interested in power struggles than building a winning team, I don't think you would have seen the investment in the 2007 team that started in the Winter and has continued throughout the season with the acquisition of Gagne. Those bold moves I believe were directly attributable to John Henry stepping forward. Granted that some of those moves have not borne fruit. Theo to his credit took responsibilty for 2006. He made no excuses about retooling, etc. He called them what they were: bad moves and mistakes. He has rebounded nicely. If we win another World Championship, hopefully this time the FO will think more about continuing to build the franchise than fighting over the spoils of victory.
As for Youkilis, he is beloved by the fans, but he is a .260-.280 hitting first baseman/ third baseman with limited power (but who could tell after the Coke Bottle shot), but he has nerves of steel and balls the size of melons. He's a great value right now, but they should probably consider trading him while his value is high and before he starts asking for Superstar $. That may not be for a year or two, but he would be a very valuable trading chip.
As for Pedroia, he has the one thing that scouts can't see or evaluate, the heart of a 6'5" warrior in a 5'5" body.