Misfire at cruise, popping/afterfire at 3000RPM

That distributor can be adjusted for the amount of advance it allows (by loosening the two screws and adjusting the window width), and how quickly (with springs).
But, if the billet dist behaves/misfires the 'same' as the factory distributor, I'd go back to the factory one again and check the idle/all-in timing and get it close to what Mattax has suggested. Focus on getting the max timing correct and let the rest land where it does - it's far less important than figuring out the misfire, and misfire isn't going to be affected by what the idle timing happens to be.

No reason for a stock distributor to not work, and it would work with the limiter plate you bought (if it becomes necessary).

I think the outer carbs are your likely culprit for the breakup, but your ignition is so out of sorts there's no way to confirm that until the timing is correct.
Unfortunately I don't have the old distributor, I donated it to a member here. Kinda wish I didn't now.

The engine didn't run any better or worse with the rear carb disconnected, nor any different with both outboards disconnected.

@67Dart273 mentioned rotor phasing very early in this thread. I read the whole thing and never saw it addressed. Has rotor phasing been checked?
I didn't check rotor phasing, because I ended up with a new distributor.