I've built a few headers for bracket cars and sprints in my many years and you always match the header lengths from the flange to the collector so all cylinders scavenged equally. That is the reason a "tuned" header look like a can of worms. You adjust for unequal spans by using appropriate sized curves. The unequal and too short lengths in your header really change how each cylinder scavenges. Don't know how you would ever get that to breath equally across all 4 cylinders. As for flame out the exhaust, watch a NASCAR race. Chopping the throttle at speed cuts off the air but increased vacuum on the idle jets so it pumps a lot of unburned gas through the motor until it hits oxygen in the hot exhaust. As for the statement: "76 CB750 all stock sept for Cycle X carb conversion" couldn't be further from reality. That exhaust changes the whole dynamic of the engine. An engine has to be balanced, intake and exhaust, and across all cylinders to run properly.
There is some good reading on the internet for exhaust header design or theory. You may want to get the welder out again.