the pipe is where you wanna start. this is what you build everything else on.
the pipe will dictate your engine's max rev, the peak horsepower, how far the engine holds peak horse, the nature of the power curve, the bottom end come on, the over rev.....
start w/ the right pipe. do your research, and make sure you get the best pipe for you particular application.
then from there you can have the jug modded by a knowledgeable builder (i ALWAYS recommend kennedy_power) who will tailor your exhaust port to match your needs, match the head design to compensate for the loss on exhaust port design, then the transfer ports.....etc etc...