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By crank do you mean the engine doesn't event turn? The Toyota Immobilizer system does not effect cranking at all, it only cuts fuel, so it still allows for the engine to spin. Please verify it is not turning over, we may be looking at more than an immobilizer concern.
Is it an option for you to remove this system. I doubt this is a vehicle issue.
Have you Tried using a different key?
So this has been completely removed from the vehicle, was it cut into the system or was it passive as in t tapped in .was th imobilizer bypass part of the artica
Remote start system removed?
Has the vehicle ever started since removing remote start? Who removed the unit?
I would follow the wiring for the remote start unit and confirm that it doesn't interrupt any wiring.I would specifically check for any open in the wiring between the immobilizer antenna and the immobilizer ECU.I will send pictures of antenna and ecu locations.
Have you checked for any blown fuses that may have occurred due to the alarm issue? If the wiring is fine as you state, the security does not go off while turning key to the crank position, and inserting key into drivers door to lock then unlock does not work, then the only other issue that could be causing this is a blown fuse.