A good story, well researched and with a good ending. I and others spent hours trying to improve the inlet and exhausts of the Triumph "new" 790cc Bonneville's engine, before coming to the conclusion that if I wanted more power I'd buy a bike with a bigger engine.. Why? Because I wanted a bike that ran equally as well at all throttle openings and that involves compromises. The sort of modifications that could be made easily certainly improved aspects of the bikes performance, but not all.
As Peter G says, tuning an engine for road use requires a properly matched inlet and exhaust so that the motor performs well at both normal traffic speed and at higher revs. Whilst there is good science that describes the way air flows down a tube in a stable system the movement of air in an inlet system is more complex as the velocity id constantly changing and is influenced by valves opening and closing. So it is as much logic as art.
Consider the manufacture of a wind instrument, such as a saxophone. The difference between one that can sound divine and one that sounds "OK", when played by the same person, is almost impossible to measure. But it is real. It is so with inlet systems, and exhausts.
The short racing inlet trumpets were also paired with very short exhausts, the system optimized for wide open throttle performance and often difficult and part throttle...
Final comment: the polished stainless tubing over the engine looks wonderful, there is something about large bore polished tubes that appeals to me!!
