You must have a broken wire or other bad connection, I'm guessing.
Well, I think I'm giving up, but there is definitely a bad or broken connection. The wiring for the two lights that aren't working comes out of a wire run on the starboard side of the hull in the lazarette at the transom and runs first to one light and then the other. There's a splice off the main line to the first light and the main line is wired to the second. There's one joint between the starboard wire run and the lights, and from that joint to the lights, everything is fine, but there's no power getting to that joint and no continuity with the switch at that joint. But that's about as far as I can go.
There is a feed running under the main cabin floor in to the area starboard of the bilge, and then it splits to power the lights on the starboard side of the forward cabin, in the main settee (fridge pump area), under the stove (no access I can find unless I pulled up the floor which I'm pretty sure is glued down) and then back to the transom. I can't access where that split happens, there's no access panels anywhere in the galley, but I suspect that is where the problem is.
The aft cabin and bathroom lights have different wire runs from the panel area (I still can't figure out where any of the runs starts from, maybe a bus bar with the different feeds out to the lights), as do the port side lights under the nav station near the forward bulkhead on the port side, and in the cabinet in the forward cabin (port.)
Anyway, a friend who is a marine electrician is going to take a look when he's doing some other work on the boat in a couple weeks. My guess is it'll take him 5 mins to figure it out or he'll say there's not enough access, just run a new wire. I now know enough that if I could access all the wires I could definitely figure out the problem, but that's not quite good enough!