You might as well just buy a set of PP'd heads if you are going to do ported heads. MHS stage 2s will run $1500 and change. I'd honestly bolt the stock PI heads on and go and then look at supercharging it down the line but that's just me.
As for automatic vs manual... RWHP is just a number, autos will NEVER make as much power on a dyno as a 5 spd will. With that said, a properly setup automatic will skull**** the stick shift in a drag race, even one making more power. The torque multiplcation of a good stall converter coupled with the speed a good auto will shift at makes the auto come off the line way harder and a lot more consistantly. Even at bolt on PI power levels a good auto will go mid 12s in the 1/4 mile. Guy at a local track near me went from high 12s/low 13s to mid 12s just swapping in a 3500 stall.
And before this turns into a stick vs auto debate... for a track car there IS NO DEBATE, the auto is the king of the 1/4. For a street car its all personal preference, for a corner carver the manual rules there.
2000 Mustang GT Steeda #0048
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.