If you're really interested in the different permutations of this decision, I wrote a blog post with diagrams and pictures that describes my thought process. You can find it here: http://bristol27.com/blog/?p=146. It's not necessary to read the entire blog post, since for the purposes of this question, you really need to only view the following diagram which shows the "improved" drainage plan:

Since the 2" seacocks are so spendy, I am now considering running the aft cockpit drains to dedicated 1 ½” seacock’s below the cockpit. Not only will the cockpit drain more quickly, but I will save $411.42 ($205.71 per seacock). The question I have is how should the aft cockpit scuppers drain line be routed? As I see it, there are two options that stand out:
Option #1 – Position a 1 ½” seacock directly below the aft cockpit scupper so that there is a straight line from the aft scupper to the drain. This would be an above the water line seacock: draining below the overhang. I’m worried a line such as this might have some back flow into the line by following waves. Also, without measuring, I’d be willing to bet that the height of the seacock + the depth of the cockpit scupper fitting would be too tall to run proper drain lines.
Option #2 – Position a 1 ½” seacock about 12 inches forward of the position of the current cockpit scuppers. This means that each seacock has a 1 ½” seacock of dedicated drainage. Also this means that the thru hulls will be lower on the waterline (or just at it). The downside of this plan is that the drain lines will decrease access to my rudder post (since there isn't much room between the new, below the cockpit fuel tank and the rudder post).
There are probably other ideas or more to be said about option 1 or 2, which is why I’m posting here. Your thoughts?