Ford fixed a lot of stuff across the vehicle lines in Sync 3.4.xxx, including the master clock and climate controls. Unfortunately this causes issues with pre-18.5 model year vehicles originally equipped with Sync 2 and 3.0.
As far as the 2011 Explorer, The value at 7D0-01-01 xx** xxxx xxxx is 21, probably should be 29 since you put a Sync 3 unit into this vehicle.
As far as the 2015 Escape, the asbuilt shows Sony Stereo DSP but no steering wheel controls for volume, etc. This does not look correct, as usually the Sony systems included these controls. This might be a 29 also if these controls are present.
The rest of the asbuilts are for Sync 2, and some of the values do not translate to Sync 3 directly.
This issue is documented on Escape, Focus, Fiesta, and maybe I’m missing one or two. If your settings for Sync 3 are the same as above for Sync 2, this could be one of the issues.
Could you post your Sync 3 values?