From PBL's notes in Risks Digest:
Under the correct checklist settings, the pitch (nose-upward angle) of the aircraft on takeoff would have been automatically controlled when the autopilot was engaged. The co-pilot who was flying rotated on take-off to a high angle. Meanwhile, Warner engaged the autopilot (which took three tries) and `failed' the left engine. It's surmised they were expecting the autopilot to return the aircraft to a precise pitch as it handled the situation, as planned. The aircraft was flying in a different control regime than planned due to the mistaken altitude-capture setting of 2000ft rather than 7000ft on the autopilot. Pitch was not 'protected' by the autopilot in this regime. Speed decayed rapidly since the nose did not go down, the aircraft was unable to maintain lateral control when it was below the airspeed required to do so, and yawed and rolled. After this situation had developed, Warner throttled back the right engine to regain lateral control, as well as regaining wings-level and nose-level. When control was regained, the ground was just a little too close.
Hope that helps.