Can you change the injection phase angle in the software? It could be fuel stand off in the intake where the fuel gets blown backwards up the intake and it acts like a rev limiter as the engine stutters because the mixture goes all to hell. When I was welding up custom intakes for rotaries, the more overlap I put into the motor, the farther away the injectors had to be away from the rotor, or in your case, cylinder. On some intakes, i could fix it with phase angle changes.