Howdy Chris and all:
Know that the air/fuel going in is wet and cool. The exhaust going out is hot/dry. Intake is sucked in from vacuum. Exhaust is being blown out from the combustion burn and piston push on the exhaust stroke. All this, theoritically, makes the exhaust system more efficient than the intake. The air/fuel mixture expands rapidly as it burns, pushing the piston down and blowing itself out the opening exhaust valve. The volume of exhaust goes up fast as rpms increase. A stock exhaust may be adequate from idle to 2,500 rpm. After that, back pressure build to the point that it inhibits performance. Header, header pipe, muffler and tailpipe are all part of the exhaust problem. Improving the most restrictive part, usually the muffler, improves the efficiency of the whole system. An improvement here helps performance/efficiency from idle up.
Typical performance intake valve diameter to exhaust valve diameter and port volume is 75%.
I did not answer you question, but this may help you find your own best answer. I don't remember the details of your engine, but in general, a bigger cfm carb will be noticeable. When you improve exhaust you may not notice a performance increase until you tune and/or rejet to take advantage of improved scavenging.
Slade hit the nail on the head. With improved carburation and cam timing, a header system will allow you to move up the rpm/power scale. Remember the air pump analogy of an internal combustion engine. More air in+more air out=more power. If the displacement is fixed, then the critical variable is rpms.
What do you think?
Adios, David