If nothing else but the
trans was worked on, I'd think that it would be, (the vibration), drive train related.
If you are getting the vibration when the
trans is in neutral and the car is parked, then I'd say you have the wrong flexplate or one that is warped.
If you are getting the vib. while driving down the road, the cure may be as simple as rotating the driveshaft 180 deg. at the pinion yoke. Whoever did the work didn't mark the driveshaft when it was pulled for the
trans work.
Ford pinion yokes have small locating tabs that lock the U-joint in position, so that it's centered, when you tighten the two U-bolts down.
It is possible to tighten down the U-joint off center if the tech isn't paying attention. That will give you a nice noticeable vibration.