That's a tough bunch to have the 2nd pick. I'd like to say Jose Reyes but its hard to take a player coming back from injury that high in the draft. The sure thing would be to grab one of those top 3 SP Santan, Haren or Lee. I think Lee is going to pitch with a fire in him this year and get that big contract the Phils weren't willing to give him. Your later pics you might want to focus one of them on a premium position player say Brandon Phillips who I think will have a great year and maybe another ace as you're not protecting any. Good Luck.
I'd go for either Zimmerman/Youk or A-Gonz, with OPS as a category instead of average, power bats get a nice boost. I definitely would not go Reyes, but if you really wanted to grab a 2B or SS, I'd go with Pedroia over Jeter, but I think grabbing one of those first three to fill out your IF slot would be really nice; those guys are all excellent 4-category producers. I would go A-Gonz/Zimm/Youk, in that order.
On the way back, I would personally like to get two more bats. Use one to get the best hitter available, and the other to either get an OF (since you start 4) or a 2B/SS to make sure you aren't scrambling to fill those positions. If Haren/Lee/JJ falls to 19 or 22, I'd grab one of them.
I like AGon with OPS as a category, but you have greater needs considering you already have Prince to man 1B.
I think Reyes is the clear cut guy it seems, but it really concerns me coming off injury.
This all leads me to think that maybe a pitcher would be best for you here, especially considering you didnt keep any. BUT, pitching seems pretty deep there and I think you may be better off to pick from the thinnest postition (SS) if Reyes is still there, then take a P (possible one of the 3 will fall to here, which is essentiall late in the 6th round) and OF at 19/22 since you'll still get good value there considering the depth left in OF and SP.
It's kind of risky, and Reyes isn't gonna help much in OPS, but you've got slim pickins at SS and it would suck to be stuck scrambling.
If you want the safe choice, take AGon for your IF slot or your favorite of Johan, Lee, Haren.