Rossiz, thanks for your update. I've been working on this since the posts began (well, mostly thinking). And, I've come up with some ideas to try. Overall, though, my thinking has landed on the following (supported by your own dyno runs):
1) Longer (i.e. stock) air horns/velocity stacks are best...both for resonance, runner length, and air conditioning (streamlining, compression, air speed, etc.). This was confirmed by a few folks I know at Redline, Top Performance, etc. and others who like to ponder fluid dynamics. So, decision 1: keep the 2.5" horns.
2) More air is better. I looked into the generic air filters which are 3.25" deep and the K&N ones which can be 3.75" but both sit really close to the air horn (.5" or .75"). This seems to suggest that there would still be a restriction, especially at max RPM) made worse by the environment inside the air filter as valves open and close. As the opening of the air horns is 2.5", I'd like the same space between the end of the air horn and the filter surface. In plumbing, that's how you'd do it, yes? It's true that air "turns" more quickly than water as it's lighter, but it's the same idea. Decision 2: more space is needed.
3) The turbulence thing you talked about is definitely an issue, as well as filtration, so in addition to lots of air, I need to make lots of it available, protect it from the heat coming up from the header, turbulence, and keep it relatively cool. I have a heat shield over the manifold already, but decision 3: add some kind of heat shielding.
I've attached my latest heat shield and have a plan to build a bracket to stack two air filters on top of one another which will give the horns the 2.5" of space I think they need. I've got the heat shield finished I CNC-ed from aluminum (see photo) and added heat protective shielding on the bottom. I will work on the brackets next. More when I'm finished!