Good job H.B..!! You did some homework and found out all those books and computer programs only get you so close.! To fine tune, you have to do the work yourself. We found that even 1/4" on intake length made a noticable difference.
Same with exhaust. When my guy made the new exhaust header pipe (to take a bunch of bends out of it). All the lengths were to be the same. Well, the dyno knew better.. The dyno instantly found it and told us all our settings (carb) were now off and the power was down, even after changing the jetting. A quick tape measurement showed it to be almost 2" short. Added the 2" and voile, it went back to where it was.
And you are correct, tuning the intake tunes more than one thing.. That length also accounts for cam specs, and exhaust lenght, and of course desired result.
I should make a separate WEB site with all the pictures I have of a bunch of race bikes, no two are the same on either intake or exhaust. If you see an up pipe that ends near the seat, that is darn short..! So a good example is look at a BSA Gold Star with a Clubman's pipe, then look at a Gold Star with a Scrambles pipe. No tape measure is needed to see the difference..! Tuning can be frustrating or it can be fun, but it does take a lot of time.