2000 323i won't start after brake change

I recently replaced all my brakes and rotors on my 2000 323i (E46). When I tried to start the car again it would only make a couple of knocking sounds
and the headlights would flash. I turned the ignition on for over two minutes to reset the brake sensors. My brother says that I probably jacked up the rear end to high affecting the engine immoblizer. If so, what do I do now? I'm clueless.
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