Toby,
You're on the right track, if the signal to the injectors becomes erratic at 5000 rpm that is why your engine wont rev higher than that. I'm not sure what inputs there are into the Haltech, but each one needs to be checked individually to determine if any become erratic or just plain bad at 5000 rpm. The MSD is a possible culprit, but I'm sure there are other sensors, for instance throttle position and manifold pressure are also worth checking.
George
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