I've had a similar situation too. Got my TJ a couple months ago, drove it for about a month, & wheeled it, never had any shakes. Put a 4" RC X-lift in it, put the same tires back on (32x11.5 BFG AT), drove it for a couple weeks, & wheeled it, never had any shakes. Got the new tires & wheels (in sig), drove it for a couple weeks, wheeled it, never had any shakes. Got the RC spacers, put those on, along with the original 32's which I saved for street use, and now it shakes at 45-50 mph. Mostly just does it if I'm going around a gradual curve. Last night I re-set the toe-in, and that seems to have helped, but I haven't driven it much yet. The toe-in was almost 1/2", now it's about 3/32". My rotor clips are gone, I've checked the spacer's tightness twice, and everything else in the suspension & steering seems good and tight. I'm hoping that toe-in issue fixed it, but if it does it again I'm gonna have the 32's re-balanced. They just came with the Jeep and I'm sure they haven't been balanced since they were new, even though some of the tread is missing chunks on the inside where it was rubbing the lower control arms (PO had 32x11.5's on stock wheels and stock suspension so it rubbed at full turn).
'97 TJ, 4.0 auto, Jeep newb,
So far: RC 4" X-series lift and SYE/CV
Swamper LTB 34x10.5 & Blackrock 15x8