Hey Bud, The rectangle port heads are highly regarded for automotive applications,will flow @7000+rpms. Like Guy Hiltz suggested, you may have to up the revs to take full advantage of them. If you want to maintain current rpm levels, the medium ports will boost torque right in the rpm range that you need and also boost low end grunt to jerk double skiers out of the water. You might find a automotive machine shop that would be willing to trade you a set of completely rebuilt medium port heads for your rect. ports(highly desirable for drag cars).
As far as the exhaust, you need to go full 4". A lower priced alternative in marine exhaust manifolds with individual runner design is the Kodiac brand. I used them on my 406 sbc with 3.5" and did a 468 bbc w/4" for a friend in his boat. I was well pleased with the end result. They are half the price of Gil, Imco and others. The aluminum casting and powdercoating is great, remove a buttload of weight. As far as the classic aluminum logs, I dig um for looks, especially polished, but a log is a log, the individual runner manifolds perform like short tube headers and a log performs like a LOG.
You may need to jet the carb up a bit after the HP manifolds resulting in more top end power. The GM manifold responds well to staggered jetting, the design runs some cylinders a little lean. Gotta read the plugs. Sounds like you got the timing pretty good.
Again the book I referred to is a good read, got mine off the shelf at Books A Million. I have been building hotrod engines for cars for a while and think I've got pretty good insight on do's and dont's, but when I started playing with boats too some years back, I had to start thinking on different terms, for instance, targeting power improvements in a specific rpm range versus just bolting together the biggest power makers you can afford on a car.
More food for thought. Keep us updated regardless of what you decide, I love HotBoats, especially the classics.