Climate control unit not working.

Do you still have the original audio unit? Is the aftermarket tuner using it's own 'faceplate' , or is it fit into the OEM one? Have you checked the fuses?

Part of the climate control goes through the factory radio. When you removed the radio to install the Navigation you broke the connection. the connections for the radio are at the rear of the radio and on the front of the radio there are connections that goto the faceplate that has the climate control. In order for the ac controls to function you would have to reinstall the factory radio.