Nice review Joe. I would suggest that some of the harshness you are feeling may be a result of the Koni's damping being set too low. Remember, you are only adjusting rebound damping, so the firmness associated with suspension compression will be constant. It is just as important to control the rebound of the suspension adequately, so that the corners don't slam down into road surface imperfections.
With my Koni/EE setup I found that the middle of the range (1 turn) to slightly over (1.25 turns) was optimal for comfort. I would imagine that since you are using the stock springs you might need slightly less damping, but I would still recommend starting at 1 turn and adjusting from there.