Glad to hear that the factory has acknowledged that there is a problem with the flat spot. I somehow doubt an ECU problem, unless someone has inadvertently loaded an incorrect calibration, or it would be happening across the range. If it was me I would be checking the things relating to throttle position first, the sensor on the pedal, the actuator at the throttle body, and then move on to other sensors relating to fuel air mix and so on. Let's face it, a naturally aspirated 2 litre engine is never going to deliver the low down torque of a turbo charged engine but it should pull well from from 2K on up with a gradually increasing push until it gets to somewhere between 3,5K and 4K at which point you should start really shifting.
I would not worry too much about the running in thing. We did 3,000 km just getting the car home so it's first service was at 3,000, and that didn't include an oil change. Most cars these days don't even get their first oil change until 20,000 km. The precision of fit and finish of mechanical components is much better than it was years ago when I first started mucking about with engines.