Engineering is the art of compromising cost and technology to get an acceptable result.
Good engineers design machines like our CX/GLs They were pretty cheap in the day for what you got, and have obviously proved to be both fun and durable.
But consider the implication of my first sentence: technology is not static - it changes over time. Therefore, ideal solutions change over time as well. - that's why a cheap 2010 bike is probably a better motorcycle to actually ride than a good 1940 bike.
That said, you had better be willing and able to re-do all the affected engineering if you want to change something basic in a complex system and get a result as good as what was there before. Most people aren't up to this. Many more believe that they are than actually are. That's why so many modification jobs end up running like crap/dangerous/covered in dust in a corner: not everybody was cut out to be a mechanical engineer.
Our engines are air pumps. Everything in the system was designed to work together as a set. If you change the mufflers, air box, H-box, or any combination thereof, you change the volumetric efficiency of the system, probably in complex and unexpected ways.
One problem we're all dealing with is that the cam grind is what it is, and it was designed with expectation of certain amounts of exhaust resonance and backpressure and intake resonance and restriction. Since there were no aftermarket cam grinds for the CX, you're left unable to alter the pumping parameters of the engine to deal with changes in the plumbing. That's why the fuel economy goes to hell with straight pipes, with pods, or both.
This sort of plumbing mod makes a lot of sense for Jim running at Bonneville - he's running the engine beyond the stock redline, so pumping efficiency goes well below stock values at cruise RPM. Increasing the flow efficiency of the intake and exhaust can do nothing but help as long as his engine is above 8000 RPM or so. It probably runs like a dog at 3500, though.
That's the difference between hot rodding and road vehicle engineering - the compromises. Jim doesn't care that the bike is unrideable at 30 MPH on the street. He cares a whole lot that it is fast and stable on the salt. Imitating what he did with your street bike will probably not get you what you're looking for, no matter what you're looking for.