Testing has been in place since 2003 and only this year did Manny get busted. He has already pointed to the fact that he has taken and passed about 15 tests that have been administered to him in an attempt to contain the usage to this year, when he was conveniently not with the Red Sox. Everyone will speculate, but until the rest of the '03 test results are leaked with his name attached, there is not going to be any evidence that he was using before this.
[Sidenote: How long until someone comes out with a Selena Roberts' style expose on Manny? It seems like there is a lot of money to be made in digging through accused steroid using baseball player's pasts these days. I don't think it would be too difficult to dig up some charming anecdotes on him, and I'd just love to know how much he tips at Hooters! Anyone want to give me an advance?]
How is the three-way trade with the Pirates and the Dodgers looking for the Sox now? Manny is gone for 50 games. That's over $7M of his $20M salary. Yes, Boston had to pay a lot of his freight and part with prosepcts, and Manny has been on fire since joining the Dodgers (.380/.490/.710 = 211 OPS+). But his replacement, Jason Bay has a solid (.299/.410/.559 = 145 OPS+) line, and that is presumably without the benefits of whatever drug Manny tested positive for.
In addition, the Sox organiztion has been largely spared the of embarassment of this going down with him still on the team. The graphics on SportsCenter and the MLB Network and ESPN.com will carry the Dodger's logo. He won't have to answer questions at Fenway about it. All those clips of him mashing in a West Coast, National League uniform really deflect the stigma away from their two World Series titles and Manny's WS MVP. That's what I care about: the Championships.
Maybe he was only using with the Dodgers. Maybe he is really as dumb as he seems and accidentally took something that triggered a positive test. However, I would be inclined to believe that you don't pick up these sort of sloppy habits in your 17th season in the league. I just wish there was some proof.