I don't think this would really prove much, but if you disconnect both exhaust pipes and just run it through the headers, (VERY LOUD ) does that make any difference? I think you are going to wind up having to do that anyway as that # 3 plug and the symptoms you describe sound as if the engine may have to come out. My 69 Cobra with the 428SCJ that is bored .065 over and blueprinted doesn't even run well until it is over 3500 RPM. The peak power is at 6300. And I had a smaller cam put in to lower that.
Ron