I would not install those bug-eyed cabin-side lights. I have them, and we always have trouble with the jib sheet hanging up on those damn things while tacking. I would go either with a bow-mounted setup or more streamlined and less snag-proned side-cabin lights (if you can find something like that). Also, I think most lappers cover the side cabin lights when close-hauled...I think (I haven't sailed the Tuna using those lights for SOOOO long, I can't remember for sure) which is not a good thing. I'm surprised that you can't find green LEDs, traffic lights these days are all LEDs, including the green ones.
I don't think GPS is very good for optimizing boatspeed on the bay. Since it measures speed over the ground that includes any current component which will confuse your speed through the water measurement. Ideally, I would use both: the difference will tell you whether you are in good water or bad, current-wise.
I use those cigarette-light adaptors below on our Pretorien, they seem to work pretty well there. On the Tuna, though, I think it might be a little too wet for those things. You can get marine quality two-prong DC fixtures at Sven's or West Marine, I think that is the way I would go for something that will be exposed to the elements-- they have little screw on covers that you can put in place when not in use, also.
If you're not going to mount the antenna on the top of the mast, I would just use a hand-held. I don't think mounting a whip anywhere but on top of the mast makes any sense... since this is all line-of-site stuff, I think today's hand-helds seem to be powerful enough to transmit to the horizon from few feet off the water. Not only that, but going below to work the radio is pain in the ass. Even on our Pretorien, I tend to use the hand-held more, since we keep it in the cockpit. However, if you intend to do much ocean sailing, where VHF range will be more important, I would put a whip on top of the mast with a standard VHF, and I would also have a handheld.
Would you put a hole in the wetted surface for a speedo?
I did. I would recommend installing as close to the centerline as possible. You usually see them installed forward of the keel (that's where mine is), I suppose to insure that it is in a laminar flow region, as opposed to turbulent flow.
Would you put holes in the hull below the rub-rail for lights, ala Riff Raff?
Either that or some kind of surface mounted light just behind the forestay. If you can find something that would not be totally obscured by the forestay... seems possible to me. Don't worry about putting holes in the boat. Fiberglass is easy to repair, and it's easy to seal a fitting in so it doesn't leak