Anytime you change the characteristics of the suspension, lift or lower, you also change the geometry of the alignment referenced to the vehicle. Rather than think a 2" lift doesn't do anything, think of a 2' lift. The farther you bring the suspension away from the frame, the more you change the relationship of the axles, suspension, driveline, etc. Yes, sometimes to many TJs, the 2" spacer lift is nothing, but other times, watch out like you have found out.
First - did you get an alignment after all the install? You have changed the caster on the front axle (the balljoint relationship with vertical) as you have drawn the front axle farther under the frame. You have also changed the steering alignment as you've needed to adjust the length of the drag link.
You got the adjustable track bars to 'recenter' the axles under the vehicle. So hopefully you've done this.
As for the rear, using a riser bracket on the rear axle helps keep the track bar as near stock length/angle, but again, sometimes the tolerances were not in your favor. Just like the front, you've drawn the rear under more underneath the frame. Most remedy the vibration by lowering the skid plate, but this in turn causes binding in the t-case shifter as it uses the floor as a mount. Lowering also hinders the recognition of replacing worn joints in the very short rear ds.
For remedies,
Alignment should work out some of the 'darting'.
For wandering, difficult to say, but make sure all your bolt/nuts are tight. Maybe the parking brake cable(s) need adjustment.
For vibration, your pinion should be pointing at the bottom of the tcase and not straight at the end of the shaft. Your axle rotates upward under acceleration. For the front, not a big deal for the spacer lift as the front ds is so long. Besides, the front has an elongated bolt for caster. But for the rear axle, the next remedy is to add adjustable control arms. You can rotate the pinion upward by lengthening the upper or lower arms. Some choose the upper first rather than the lower. Once you get arms, I'd remove the skid plate drop. You loose the lift benefits by lowering something you've lifted, especially something that big in the middle.
Take a look at these and hopefully this will remedy your situation before you get bigger heavier tires (and wheels).