Spoke too soon...
It's still making that awful noise, only when in gear, only when from a stop, only when I slowly accelerate, and it still hesitates when it happens. Give it more gas, and it catches up with itself. But, still, intermittently.
I re-pressure tested the intakes after I installed the Z1 Motorsports breather tubes, and there are no leaks, also got under the car, and except for a small leak at the passenger side muffler (that I was able to tighten and fix) there are no leaks at any of the other flanges, no leaks at the 02 sensors, and no CEL or codes. Even when the issue occurs, there's no CEL or other warning light.
Gas mileage is good, power at WOT is good, and no other weird noises.
I'm at a loss on this.