The only positions where you want to give the 2004 squad a clean advantage are C, DH and LF. The 2009 version has clear edges at 2B, 1B, and RF.
Call me a homer but considering what both guys actually provided over their tenure here I'll call OCab and AGon a wash, and the aging third basemen with burgeoning lower body problems are a wash as well.
I'm not even sure where to rate Ellsbury and Damon in comparison with each other. I have no idea how to handle the speed vs. OPS question and Damon had a career season in '04.