The secondaries open via a cable from the small box in the right front of the front head, it's covered by the plastic panel on the front of the engine. the cable goes in under the throttle body and a gizmo there opens the secondaries. Obviously something has happened to the cable or gizmo. the butterflies themselves are real simple (a pair of long rods with 3 each throttle-like valve) and are not likely to be at fault. I have never taken the gizmo apart, only looked at it 2 years ago. Don't fotget the engine will not rev in neutral over 4,000 rpm if you are playing around with the cable etc.
