If hood clearance is a problem Chevy made some half decent low profile aluminum dual plane intakes for the Corvette and others. You mentioned square port heads, if they are similar to the Chevy high performance square port heads from the 60s-70s they may not be your best choice as they are made for higher RPM. Some of the oval port heads actually build better lower end torque and throttle response. Modern headers are much better than they used to be for sealing and exhaust leaks. They will make a big difference if combined with a 2" or better true dual exhaust. You will limit the benefit from the other mods you mention if you choke the exhaust.

Pat