wow that's an in depth league, i dont know much about the minors except those few prospects that get the most attention.
I like the idea of building around pujohls. And i like you having ss ramirez and 2b phillips for your infield. I'd keep holliday and hermida for your of, they should be good.
In pitching id keep cuapano and coffey.
Most of the others im not familiar with enough to give an opinion, so ill leave that to others.
id go for some of the good young pitching prospects that are a year or two in the bigs, like Haren, Cabrera, Bedard, E. Santana, or Young of SD.
or some other young pitchers that may be reasonably priced yet more expensive like harden, webb or c. lee, maybe patterson.
hope that helps, good luck