I'm so glad someone (
@StG58 ) mentioned the Tacoma Narrows Bridge. Its still taught as a lesson in Mechanical engineering (At least when I was in school in the late 90's). You cannot talk about resonant frequency and natural frequencies without thinking of that particular lesson (at least I can't).
I haven't done much research into the issue, but it seems to be predominately Rubicons with Auto transmissions, right?
@bobthetj03 has vibs too, but he has a sport, manual, 231 T-case. The theory of the skidplate acting as a "speaker" is interesting. Would be an easy theory to prove/disprove though. Just fill it with sand and go for a drive. See if the vibration changes. Increasing the mass dramatically should move the natural frequency around.
To me, this is kind of like a fire. You need three "legs" to keep a fire going. Fuel, Oxygen, and Heat. If you remove one of the legs, the fire goes out. If, as
@psrivats is saying, you have a cumulative effect happening, can you remove one of the legs and control the resonance?
It sounds like it to me. Will be interesting to note if Chris, with his Tummy Tuck and dramatically different from stock suspension experiences Vibs? If he does, that tells me its 100% drivetrain related.