Both models will work but I think the problem will still be present with the CRC-2000. I think the root problem is that the input I/O cell on the controller chip is an open drain I/O cell that has not been connected properly. If you were to measure the voltage on an open drain I/O cell with nothing connected to it the voltage would be indeterminate. It could be at 0V or maybe the same as the battery voltage or anywhere in between.
So for example if you have a clutch switch such that when the clutch pedal is pressed the switch closes and completes a circuit to ground and you connected this switch to the CRC-1000 without a pull-up resistor the voltage at the I/O cell before the clutch pedal is pressed will be indeterminate and if that voltage happens to be below the ON threshold (active low input) then the controller would think the clutch pedal is being pressed even when it is not and the cruise would not engage.
A possible reason why the cruise only works when the MPVI2 is plugged in is because that circuit shares a common ground with the CRC-1000 which can change the indeterminate voltage just enough such that the normal voltage before the clutch pedal is pressed is just above the ON threshold and everything works. But most likely you would probably see some random failures even with the MPVI2 plugged in as changes in operating temp, humidity etc.. could change the voltage just enough to cause it to fail. So in this example the fix would be to add a pull-up resistor to the battery on the I/O cell such that there is no indeterminate voltage before the clutch pedal is pressed.
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