I'm also building a Guillemot and will be faced with similar decisions soon. Here's what I think, based on my experience with my Chesapeake 17. I agree that there should be a way to hold a paddle for a paddle float re-entry. When I tried to re-enter my boat from a practice capsize (in calm water) I wasn't able to do so without a paddle float. (My legs are too long for a Cowboy entry.) Chesapeake suggests a rectangle of bungies behind the cockpit, with additional diagonal lines from the corner - kind of an X inside a rectangle. It has held the paddle/paddlefloat rig quite securely during practice self-rescues. I suppose if you have a bullet proof roll, you might consider paddle float rescues unnecessary, but I don't even have a bullet-ridden roll. Like another person said, those bungies also make a nice place to keep a paddle jacket so that it's easy to get to when you need to put it on or take it off.

The bungies in front of the cockpit should be as close as possible - to make it easier to reach whatever you keep there - without interfering with the accessibility of your spray skirt release strap. I keep a deck bag there on the first X, and put my pump under the second (forward of the bag.)

I also have a rectangle of bungies behind the aft hatch. This holds the shafts of a two-piece spare paddle. The blades fit under the bungies behind the cockpit. I think it's pretty necessary to carry a spare paddle when you're in exposed waters, not only in case you're main paddle breaks, but also because paddlers (who, me?) have been know to have brain farts and drop their paddles, or have them come loose from under a bungie where we've put them while we adjusted our glasses, or heeded nature's call, etc. In windy conditions I don't think it takes long to be separated from one's paddle, and paddling to it with your hands seems likely to be unsuccessful.

I'm also thinking of putting a perimeter line in the front and back of the Guillemot (and retrofitting my Chesapeake similarly.) In the case of a capsize, you need to grab both your boat and your paddle. I want this to be as easy as possible. If I'm near the cockpit, I can just grab the coaming, but I think it might be prudent to have some lines fore and aft to grab.