If it were only my car, I wouldn't be saying much, but seeing as a few people with completely stock cars are having the same issue. That tells me the tune isn't necessarily to blame.
The MAFS is calibrated a certain way. It sends a variable voltage signal to the ECU to account for how much air it sees. An aftermarket tune can't touch this calibration. Aftermarket tunes deal mostly with the reference maps the ECU uses to control the engine. Fuel trim, ignition timing, variable valve timing, temperature correction, etc. Tunes from individual vendors like @
Visconti take the stock maps and adjust the values to obtain more power that may have been conservatively tuned out from the factory.
The problem we are having is from 1000-2000 RPM. I doubt that specific RPM range of the maps were deviated from stock values by anything drastic enough to cause the issues we are seeing. They aren't a target for the power band. I mean how many times do you see 1000-2000 RPM while doing any kind of racing/aggressive driving? Visconti doesn't even show this range on his dynos.
The point of failure in this equation is the MAF reading. It's the only thing that could change the way the ECU could react enough to cause the problems we are seeing. Resonance is a factor and all, but not enough to cause a WOT motor to lose that much power. The manifold air pressure in my log was high enough to indicate that sufficient air was available to the motor.
But you are right in some regards. I'm certain a tune can fix it. However, it's a hard thing to swallow for people who just wanted to spend the 250$ on the intake without having to buy an ECU tuning kit just maintain day to day drivability.
I'm almost through my tank of e85. I will be filling up with 93, flashing to stock, and doing some more analysis. But I feel the result will be the same.