How many teams in the league and how many keepers do you get each year?
If it's a 12 team or less league, then frankly, I don't think you're team is that good. The good news is, that gives you a chance to think long term. Sort of think of it as a 3 year plan. Basically, I would punt this year and over the year, trade away your aged talent and get more young guys. Berkman I'd keep because he should still be in his prime 3 years from now. You've got prospects, but prospects aren't the same as young proven players... You need to try and get guys like Miguel Cabrera, Carl Crawford, Feliz Hernandez, Guys in their early 20s who are already proven commodities... Guys like Pedro, Hoffman, Bonds, etc... 3 years from now they'll be history, trade them now while they still have value.
Getting this team good though will take patience... You'll really need to analyze these prospects closely over time to see who's the real deal and who's a flash and the pan... For young hitters, look for improving trends in their stats, like walks per inning... that means they're learning to be selective. a young player with a good eye is generally better than a young player who has power but strikes out too much... Power can be developed over time, but it's harder to develop a good eye.
For your pitchers, I look for either high K per inning #s or unnaturally low walks per innings.
And don't too much stock in minor league stats.... They're helpful to a degree in that they eliminate the non-hackers, and you can track improvement in certain skills, but a lot of times, young players with extreme athletic ability can coast through the minors simply because their opponents are so bad but when they make it to the show, raw skills aren't enuf, they'll get crushed in the show and disappear, never to be seen again, while steadily improving but not overly impressive guys can overtime become quality major leaguers...
Occassionally you get you're freak of natures like Pujols or A-Rod. but most great players in the league got that way over time. Spotting the stats that show those guys rising up the ladder is the key in a long term keeper league....
It's what got me guys like Cabrera, Crawford, Chase Utley, etc... you need to find those guys and lock them up just before they become great players.