Well this sounds like a great undertaking and I wish you luck. Hope you have a flow bench, engine dyno, and a lot of time.
The stock system is pretty efficient for a street motor, it just needs to be massaged as a package, Cleaning up the port entries after the throttle bodies is a big help. The turns are sharp, this hurts flow at higher rpms. Port matching the lower to the upper also adds improvement to flow. A bigger issue is the oil vapor that you get from the crankcase ventilation system that is contaminating the combustion process. The used manifold I picked up was all slimy on the inside and it took a lot of degreaser to get a clean enough surface to port. For the money and time, improving what you have is probability the best bang for the buck. For a race engine, different story.
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