Reason I asked 'why aluminum' --- the fact is, no aftermarket manifold will perform as well on a street Pontiac than a cleaned up, port-matched factory cast iron manifold. The notion that after-market aluminum will always be 'better' is what I call "Chevy thinking". True, it will save you some weight, but that's it. In terms of torque and power in the street Pontiac rpm range (5200 and below), that fancy aluminum manifold is going to cost you power, not make it. This fact has been proven time and time again through actual testing. Fact is, Pontiac didn't gain its reputation 'back in the day' because the factory engineers were idiots. Pontiacs are torque engines, and it comes on early in the rpm range - nothing feeds that better than a clean dual plane intake and that's just reality.
It's the same reason they don't need (or like) a lot of gear to be quick. My 69, at about 4000 lbs. race weight, has a best e.t. so far of 11.86 @ 113 - that's on pump gase, with 3.50 gears and running the trans in Drive - and it shifting at 5000 rpm. I can drive the car anywhere I want, and do.
As far as the water passages in your block, don't panic yet. For whatever reason, I know that there are passages in the heads that meet with blind passages in the block - do sime internet searches, grab some books, and look at other blocks. You'll probably find that you're not as bad off as you think.
I run headers on my car too, but honestly unless you're trying to get every last bit of performance out of the engine it's very hard to beat the manifolds like you have. For about the cost of a good quality set of ceramic coated headers you could have a reproduction set of those manifolds from Ram Air Restorations - "most" of the performance and none of the fitment/clearance/longevity of headers. Your choice on that deal.