I did a similar mod but with much smaller holes.
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This with fuelx lite and just an Arrow endcan.
I see you have good hands on you, as a toolmaker I can see the effort and time you have given to this fix, I used to do the same with hacksaws, files, emery paper, I did it cause back in the day I was skint and enjoyed a wee project. KTM as correctly stated have an R&D dept to produce the best airbox solution, but there arms are tied behind there backs, having to meet nearly impossible regulations, noise control, emmissions, Euro 5 tech, I believe there is a lot of maneuvering between adjustments air in and gas out by removing Euro 5 parameters.
My understanding of the air flow there is a small rectangular area below the original filter that draws the air via back pressure through the filter, you would be surprised how little air is drawn from under the seat, I bought a high flow filter which is the most important fix, but in additionI bought this (China) it arrived yesterday, thinking it was a plastic item but was shocked that it arrives in 2 pieces both CNC machined out of billet alloy, comes with high density foam (red) and medium density (yellow) + stainless steel screws.
I really dont know how they do it £14.99 with free delivery, sorry I am drifting guess what I wanted to say when you take in the cost of grinding discs, drills, materials you have a lump of I guess 3mm alloy, mesh, nuts bolts, foam etc oh forgot most importantly TIME, old men like me go China + still have original to revert back, incase next buyer unhappy and lets face it they are always unhappy