Okay... Hmm...
Cars have gone for years without needing a balancer on the tail of the transmission. So, it CAN work...
Thoughts:
It appears that Ford found something with the drive shaft design that they changed for the last couple of years that they used this T-5. ...around 2008, 2009, 2010. So, what style is your new drive shaft? If it was one just like the original then, maybe continued vibration might be expected. If Ford didn't supersede the balancer flange with the plain one, they probably didn't supersede the drive shaft with the improved style either.
Also, make sure the rear mount for the transmission is pretty firm.
If all else fails you might need to do a "pinion angle" check comparing the angle of the flange on the differential to the angle of the flange on the back of the transmission. They must be parallel to reduce vibrations.
Has anything been done to the differential that could affect the angle of the rear flage, or has the car been lowered by chance?