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To answer your concern about the serial communication. If you manage to connect the LevitatorHost, and tune your PID, then the serial communication is fine, as the LevitatorHost is using the protocol described in the firmware.
However, you can only have one connection at a time. So you cannot connect the LevitatorHost AND another serial console.
Hope this anwser that part of your question.
Regarding your sensor. Reading your description, it seems that it is fine (according to the reading you're reporting: 2.5V at rest, and increasing/decreasing when approaching a magnet.
Concerning the auto standby/shutoff, (and the whole system polarization), I would recommand you to read the User's manual.
The procedure, to orient the magnet, configure the controller, etc...) is explain.
Maybe it's not clear enough and if you have other questions, I'll be happy to answer.