So I disconnected the battery again thinking it would "reboot" the PCM, no luck, now it runs like crap, RPMs are hunting and trans is shifting harsh.
Above comment is normal. Fuel trim adaptive memory and trans shift adaptive will take a small while to relearn as Billr wrote. As for the steering a 1/4 off, that is quite significant and I would suspect it would have coded a steering wheel angle sensor code.
So, I would look at the work order and see if you can find the recall #. If they replaced the steering angle sensor as well, it was badly done and I am extremely surprised it did not code that. Post back the recall number and I will study it.
Also, what type of code reader are you using?
Upon return I noticed the steering wheel was at least a quarter turn off center. I could tell they disconnected the battery and this vehicle has electric steering, so could the steering have lost it's calibration and needs to relearn?
As for this comment, there is no way this steering wheel is off center because the steering gear lost battery power. There is still a physical link that makes it impossible to be a 1/4turn off unless someone took the rack out, or took the steering wheel off and put one or the other back on and did not mind the markings or did not center his steering wheel before removal of either one.
In the following picture, you will see the rack and the pinion shaft that is bolted to the column.
Other types of electric steering cars are completly separated from the column. Not your fusion. There is an assist motor off to the side, but it does not affect wheel aligmnent per say. There is a zero center relearn that always needs to be done when a rack and P/S module is replaced, and also when a steering angle sensor is replaced. Picture in PDF below.
I also know there is or was a recall for the steering gear(rack). So maybe they did that as well. I don't know. But if your steering wheel is off a FULL 1/4turn, something was physically removed and not put back to center and it has nothing to do with a module reconfiguration. Cuz even if the steering angle sensor is not reporting zero or the module is not configure, the car will still be straight if nothing was psycyally dismanted in regards to steering components.
Hope this helps, and YES to all the other comments, that ford dealership is responsible if you were/are sure nothing else was done to it after they touched it for the passenger airbag recall.