RE: header length for pattern - max RPM or not
The flat back pipe has a converging cone too. You just can't see it. It is the converging cone that slams the pressure, some unspent and spent fuel back into the cylinder head and supercharging your engine.
You seem to be a little overwhelmed with all the advice at the moment. I am as well.
Tuning an engine with a tuned pipe will take some time to get the feeling for it. Be patient. I agree with Chris... I would pull out like it sounds you have done.
Have you read Dean Pappas's article on tuning for max performance, not max RPM? I can get that to you if you would like to read it. It is the most succinct, easy to comprehend, easy to follow write up I have ever read on the subject. It explains how everything works too! But even then, educated trial and error are still your best friend.
I am just beginning to learn all this stuff myself. Jim Oliver is an amazing help on this matter.
Brian