Check the harness that goes around the head under the manifold to the sensor. They tend to wear and short things out. Also sometimes it's not the CPS but CMpS (cam sensor). The run on the same circuit and could annoy one another. I would definitely check the harness though..I have never heard of a staged PCM throwing random codes for no reason.
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Base 4D, 2.4L swap, 2.0 cams, SRT turbo, 52mm TB, gauges and 3.0 unmodded intake, BOOGERS! and Megasquirt! 250Hp to the ground.