Toby,
It may be time to telephone Haltech. You haven't mentioned the MAP sensor. Since you are depending on that sensor to do most of the controlling, it should be checked. If nothing else, just monitor the voltage out of the sensor. Possibly it has a bad spot at a certain manifold pressure. Outside of that, I'm out of ideas.
To others reading this post, if this were an EEC IV system, it would have self diagnostics & would actually tell us which sensor was out of range. With a scanner, such as the Autoxray scanner, you can run real time trends on each individual sensor while the engine is running, including while you are driving the car, and visually check the performance of each sensor.
George
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