Ideally it would be best if someone from the DS2 faction could chime in.
However, on first reading your summary makes sense. And yes, I would start with the place where the uphaul cable exits the trunk. I've sailed on a DSII and while that one did not have issues with water between the trunks, it had a lot of water gush out of that uphaul opening into the cuddy and into the cockpit from there. In your boat, if I venture a guess, the opening to the cuddy may be sealed a bit better, forcing any water into available cracks or openings between the hulls. A corroborating sign would be if this "leak" requires the boat to be in motion.
I believe that the repair you mention can be worked without dismantling the CB. You would need to access the uphaul location from within the cuddy. If I'm correct, you do not need to lift the boat from the trailer or take it out of the water.
Second guess would be a leaking CB pivot plate bolt. This leak does not require the boat to be in motion, but having a force on the CB to twist it might change the geometry to facilitate the leak (and it may be weak, or not existing, without that assistance). You should be able to view this area with the inspection ports open, and perhaps confirm visually that water is coming in that way next time you sail.
You should be able to seal these plates without fully removing the CB. It should be possible with the boat on the trailer, to loosen one side, lower it, apply suitable caulking and reassemble, then do the other side. Or you can beach your boat and tip it over (
careening).
From my reading I would think that butyl tape would make a good sealant for the purpose. You would form two rings, one around each hole through the fitting and perhaps even a bit around each screw head. Butyl never gets fully hard, so you shouldn't need to worry about a crack later forming between sealant and plate. Whatever you do,
don't use 3M5200 because you just make it impossible to ever remove the CB in the future.
PS: that's as good a bit of second hand advice I can give you, but I'm hoping it gets you started in a good direction, even if we don't hear from any actual DS2 owners.