Was the factory harness for the stereo untouched when you started? If so you either have the wrong harness or you didn't do the coding right from the harness adaptor to the new stereo adaptor. No wires need to be cut to convert the stereo system from the 3 piece monstrosity to a normal one piece head unit. If you are having problems with the HVAC now, I would start at the source and check the connections on the HVAC control unit.
A wire could have been pulled loose when you were removing the old stereos control head unit since you have to partially pull out the H
VAC controls to remove the head unit. Everything you need to make your stereo work properly is in the 3 cable connectors clustered together in the stereo amp under the dash. all you need to do is connect your new stereos pigtail to the aftermarket harness adapter and then plug those 3 connectors from the old amp into the new single harness adapter, it's that easy.
The proper harness adaptor will have the wire coding on it and you just match it up to the wire coding to your new stereo's owners manual (some wires may not be used).
These are the 3 cables that came out of the power amp/brain of the factory stereo found under the dash on the drivers side. These are the 3 you want to plug into your new harness adaptor.
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