Jibbby, you find yourself locked into the mindset that bigger must flow more and must make more power. I am not sure anything I say no matter how well intentioned will change your mind.
Alas, I will try to illustrate.
Who in their right mind would spend a ton of money on headers and installation and not touch the rest of their stock exhaust system?
Actually, I recommend to MOST GS4xx owners too keep their stock Y pipe. These cars make around 60rwhp MORE than early SC400s stock. 70-80rwhp after the header install. The stock GS4xx Y pipe has the same dimensions as the early SC400... 50mm twins into single 60mm. Some have ran 350+-rwhp with superchargers on the STOCK Y pipe.
I am CERTAIN a better than stock system can be designed BUT most will not know how to do so. I have stopped recommending bigger pipes for most cars.
...See my point...So my post is valid and does apply even with my after market exhaust setup... Greatly Increased exhaust flow often results in low end torque and or lowend power reduction in most motors, and that is common knowledge... However, the upside is the topend is usually greatly increased...
What exactly is "greatly" increased flow or power? How do you know? What testing? What was the before and after backpressure at the exhaust port for the power curve?
Don't take this as an insult as your "feeling" is common and understandable just misapplied. Consider Bernoulli's principal often refered to as the venturi effect. As the air speed increases the pressure decreases. This is how an airplane wing creates lift and a carburetor pulls fuel from the float bowl. The concept doesn't "feel" right but is inarguable.
Another "visual" would be a modified carburetor. Carbs are rated in CFM (cubic feet per minute) of flow at a given pressure drop (pressure above carb higher than below). Take for example a 750 CFM carb and smooth and improve the aerodynamics through the carb. Even with the SAME diameter butterfly valves the CFM rating goes up... maybe to 900 CFM. The pressure drop is the SAME for the testing so the ONLY way to make this happen is increase the velocity. Now, the carb will support MORE peak power but have the same internal diameter at the butterflies.
The SAME thing can be done with exhaust. A maximized 2.00" system can flow as much as less than optimized larger system. In some cases MORE if the larger system is poor. It is not always easy to spot a POOR system without understanding WHY and HOW the systems ACTUALLY work. Now, with the exhaust you want the smallest size that will support the peak power. Any larger will not make more peak power and will only hurt power everywhere else.
Proper fitting upgraded exhaust may be the trick, but not every one properly fits their exhaust just right, they just go with bigger piping then what is needed, straighten it out, headers short and long, etc.. and in the end they hope for great results..
You are right, this is what most people do and of course the key word being HOPE.
I am sure JB, that you can setup a highflowing exhaust system on any SC400 that may not lose any lowend low rpm power... Then again I don't think the topend power would be as great as mine either.. Finding a good balance to all mods can be tricky at times..
I dictated certain key parts of the design of the S&S headers you are using (1.5" primary size, merge intersections) with the goal of great peak power without low rpm power loss. I would be glad to take you up on your challenge giving time and funding.
Here is a real world example for you to consider:
There was a member here that put the S&S headers on his early SC400 along with dual 2.5" into a Dr.Gas 2.5 into 3.00" Y pipe and then back into dual 2.5"s. That system would flow more than yours. He was very dissapointed in the torque and midrange. He replaced it with dual 2.00" duals into a 2.5" center pipe WITH a single mid cat and back into dual 2.00"s. He reported the car came ALIVE and was faster EVERYWHERE. Go figure.