I put a 3" skyjacker lift on a 92 MJ yesterday that consisted of coil springs, shocks, track bar drop bracket, and control arms for the front. When driving straight, the steering wheel is rotated 90* clockwise and the truck pulls slightly right. When I was driving on the deerfoot the front end started shaking violently. It felt like I was driving over moguls. I wasn't able to get an alignment on a sunday so I still have to do that but I doubt that was the problem with the shaking. I'm guessing the pitman arm has to drop lower but I'm not 100% on that.
And what places will do the alignments? I doubt that most places will do them with aftermarket parts. The first places I'll call is national and modern motors.