Chris,
Great looking rig!
Sculling is about the only type of Duck hunting I have yet to try. (although I sorta have a self-invited invitation from a great guy I know from up North).
I like the craft's name too!
I would patch those hole with Dura-Glass Bondo. Just make sure when you do, that you work it from the bottom wherever possible too. Clean the holes, feather out the edges a little with some course sandpaper, mix up your bondo, spread it in the hole, also working it from below, let it set up until it gets sort-of "Swiss Cheese consistency", carefully remove the major portion of it with a cheese grater type rasp, then let it harden all the way and sand to a finish. If you spend a little time on them, I guarantee you'll never be able to find them when you're done, and they'll last forever. When I say "work it from below, I mean just that. Spread it from below with a putty knife or even your finger. You just want to make sure it goes all the way thru on both top and bottom. On the scrapes, do what you can from the top. Remember to clean and blow any dust out of the holes and scrapes. Acetone is a good cleaner, but be careful with it. Denatured alcohol would probably work too. That's what I use when working with Corian countertop material.
As far as Starboard, I can only guess as I have no experience with that material. I would wonder about paintability maybe? Sounds strong.
When I have towed either my Layout Boat or my Sneakbox, I've had real good luck with a "Y" harness. Attach each leg of the "top or open" part of the Y to each corner of the tow rig, then connect the bottom leg of the Y to the towed boat bow eye. My harness is probably ten feet on each leg maybe?. Just have to be careful when you stop, that the towed boat doesn't crash into the towing boat. A little practice helps.
Good luck and keep the photos rollin'
Jon