I also have a F150 Coyote takeout and I can confirm that there are differences between it and the 2014 and earlier models. Here's something I spotted and posted in my build thread:
It looks like the new plug (and by proxy the controls pack), has wiring added for the CMCV hardware and sensors in the new intake setup. As far as I can tell, that's the main difference in the main plug.
When you say "did you get the ford motorsports replacement harness?", which part number are you referring to?
Since I'm using an AEM Infinity standalone, I swapped the harness for the earlier model year crate engine harness to save myself tons of rewiring. Comparing the location of things, there is a single wire sensor and plug attached the DS intake cam position sensor which looks to be located on the PS intake cam position sensor in earlier years based on the harness. This should be in the same location for the Mustang harness.
You will find that the oil pressure and oil temp sensors are different between the Mustang GT and the F150 as well as the oil cooler, front timing cover, alternator, and the round plug on the harness you mentioned. I'm pretty sure the controls pack can still work with the F150 alternator (which is different than the GT both in location and pulley alignment). The oil cooler has two separate sensors on the F150 and a combined one Mustang. It possible to swap out the oil cooler and it may be possible to splice the wiring harness with the correct plug for the Mustang sensor there.
When I get home, I'll take a look at the circular plug and where it leads. It may be that you can simply remove it if they are solely dedicated to the transmission. Still, I'll try to trace the routing.
Oh, and as for internal differences, I believe it comes down to the intake cam and the half point lower compression pistons. Both can be accounted for with a tune. You can either swap out the intake cams with the stock Mustang ones and leave the stock tune since the slightly lower compression will decrease power, but shouldn't be likely to cause damage.