Sounds like you are working through the standard checklist... When I had the shakes it ultimately was the CV shafts like Randy mentioned. Although they seemed OK, they were out of balance enough to transmit a vibe. I thought at first it was the bearing/hub assemblies - so I had new ones put in at 80K and still had the shakes. Then I had JE Reel rebuild the shafts and they things smoothed right out (this was way back when that was the only option other than OEM ones). Now you can get shafts fairly inexpensively...

I mostly felt the ball joints and tie rods going when at low speeds while turning.

TL

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95 YJ 2.5" RE lift and 32's, Posi-Lock, 4.10's with a Tru-Trac up front, M8000 winch, CB, gear and what have you...
RIP: 02 KJ LE