Water cock

Yes its okay. Just know that your blend and mixed air will never be 100% outside air temperature. It will always be slightly warmed.

Mixed air? I don't understand what you mean.

Is the water cock even doing anything with the heater core bypassed? will the electrical sensor on top do anything?

The sensor on top gives feedback into the whole automated climate control system. The system will function without it, but with less accuracy.

If you are bypassing the heater core, you have no need for the water cock. Take it out.

Thanks for your help.