Install a high frequency accelerometer on the car and make a run.
Use FFT (Fast Fourier Transform) software (you can find some free versions on the internet or I'm sure ATI has this software) to break down the vibration to individual frequency and amplitudes. Then take the high amplitude readings and see what frequency is associated with it.
For example, if the high amplitude vibration frequency is 13.3 Hz (13.3 times a second) at a time when the engine RPM is 7000, the alternator RPM is 10000, the trans. output shaft is 4800 RPM, the rear axle RPM is 800 (13.3 revs per second), you can focus on things that turn the same RPM as the rear axle (ring gear, side carrier bearings, axle bearings, brake rotor, wheel, tire).
Whatever you do, don't change the roof. That's not it.
Here is a cheap accelerometer that works great. I've used mine for analyzing vibrations in high speed machinery as well as vibrations when a putter hits a golf ball.
http://www.gcdataconcepts.com/x16-4.html