You've assembled a very impressive squad and like the other poster mentioned that pitching staff is ungodly. Between you and the other team's pitchers you posted there must be a huge drop off in quality of the remaining teams.
Am I reading your question correctly, you can keep up to 18 players before this year's draft but just want advice on positions to target as opposed to what players to keep? If I look at your team the glaring weakness for me is at RP, besides Papelbon you don't have a bona fide closer. Also I'd be a bit concerned at 2B and 3B those two players are injury risks. You can't expect those #'s again from Berkman either.
What I really like (besides your starting pitching) is the up and comers in OF - Trout, Jennings and Heyward. They should be lynch pins in your lineup for years to come. Also Castro at SS is nice, even with a crappy hitting lineup.