I don't want to drag this on either, hence why I posted the link. I'm assuming you haven't had a chance to really look it over.
In a nutshell, the long pipe to the back of the car has nothing to do with scavenging, that's the job of the header and collector. You want the pipe to be as big as possible as to not create more losses, post collector. Therefore, the bigger the better. A smaller pipe will not make for less losses. You make a lot of assumptions about exhaust dynamics that are just not true (explained in sticky). I don't want to take this off track, and we both agree that this is not your problem.
As far as your running issue goes, start simple. Check the charging system and make sure it kicks out the proper amount of voltage. Then check each ignition component for proper operation, checking timing is the last thing you'll do here. After that, and maybe a valve adjustment, go to fuel and carburation. Cam timing would have to be way advanced to cause such a seemingly huge hit on performance. Retarding the cam will shift your power curve to higher rpm.
Also, make sure to check throttle linkage and the pedal stop.