How many of you are Sports? The sport has a vibration when accellerating at around 20mph. I have talked to a few techs and they all told me it's normal, mainly because Ford can solve the problem. Not sure how true that is, but mine vibrated when accelerating and was solved accidentally at about 30k when the Ford replaced the pinion shaft bearing. The vibration has to do with the rear end. Check your shaft and u-joints. My X came from the factory without tranny crossmember bolts and it was loose for about 15k until I caught it. Check those as well.
Also, if it vibrates when you're breaking then it may very well be the front end. You said it vibrates when acc and braking. Check your front hubs. Jack up each side and try to rock the wheel back and forth. If it moves then you have some stuff going on there. I would start with the hub first. That is what your wheel bolts to.
Lastly, check to see if your tires are balanced correctly.