If you pull the header off and place a straight edge across the ports you should be able to see where it is warped. Most headers have a weld bead built around the port and you can build up the low one and file it flat to match the rest. Its a pain but it worked on my blockhuggers. Also use the black felpro exhaust gaskets and don't over torque. Run the engine, cool it down then re torque.
Live long race hard