[civtehc]

I’m assuming your truck is a 11-12, did you use a 13-16 cab floor harness, if so I would double check the large connector wires that they match up when you spliced the plug in, there are some same colour wires just slightly different diameter, the ambient air temp sensor is in the passenger mirror the wires run for that are in a different direction, you’ll need to run two wires to a plug under the drivers side dash by the obd2 connector it does not go to the BCM, the ambient air temp goes to the PCM
Passenger window needs to be reworked at both drivers and passengers side plugs at the cab connector
Not sure about your hvac issue maybe a failed motor
My guess is some of the power wires are not connected properly at that large plug on the drivers side kick panel

 

[civtehc]

Also is your as built module data all matched up to a 2013 with similar options? Force reset your abs module?

 

[civtehc]

All the module data needs to match, changing the BCM changes the vin programming in all the other modules, they won’t communicate very well, you’ll need to program the modules as built data to match, if the truck you got the parts from was the same options as yours or close use that in on fords side to get the as built data and program it.
I’m going honest if you’re not handy with forscan or as built data this might be tricky as it’s required to get it all to work correctly.
I can’t see the shifting issue being directly related to the swap unless the shifter cable is in correctly or something