Agreed. You need to have the PCM tuned for the proper gear ratio. The original HD trans came with 2.93 gear ratio and the replacement transmission has a 3.29 gear ratio. Your two options are taking apart the transmission to put the proper gear ratio in or to have it tuned in the pcm to the current gear ratio.
In the diagram below you'd need to change that piece to a 34 tooth VSS reluctor wheel.
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