I can definitely see the Ellsbury - Crawford - Pedey top 3. And, in all honesty, is there really that much difference between having Crawford bat 2nd and Pedey 3rd vs Pedey 2nd and Craw 3rd?
I will admit, though, that right before Pedroia got hurt last year, when Francona was hitting him in the 3 hole, I really really liked that idea. It's not unreasonable to think Pedroia will hit 18-20 HR, and hitting behind Ells and Crawford, he could drive in 90-100.
Here's my take on it, though. If you're dead set on hitting Pedey or Crawford 3rd, and you really can't go wrong with either of them, I would look at stats with RISP as the decision maker.
Pedroia (2009, last healthy full season)
.327/.418/.440/.858, 3 HR, 55 RBI. 150 AB's.
Crawford (2010 obviously)
.359/.400/.538/.938 2 HR, 63 RBI, 156 AB's.
Like I said, you really can't go wrong either way, but I think Crawford may be the better option in the 3 slot.
As far as the whole LOOGY vs your 3rd and 4th hitter (CC and Gonzo), well Gonzo last year hit .337 vs LHP, better than he did vs RHP, so a lefty specialist isn't going to be that effective against him, and if the biggest thing we're worried about is getting into the 8th or 9th inning and having Crawford - Gonzo - Youk up, and we're worried because they're bringing in a LOOGY, I think we're going to be fine.
Gonzo's 2010 stats vs LHP
.337/.424/.513/.937 8 HR, 33 RBI, 199 AB's.
Youk's 2009 stats vs LHP
.309/.435/.518/.953, 6 HR, 22 RBI, 139 AB's.
So Gonzo hit lefties just as well as Youk hit lefties, so throwing a lefty vs Gonzo is going to be about as effective as throwing a lefty vs Youk.