Even though our local 4WP does a great job on most things, I have not had good luck with their alignments. After the first one they did on my jeep, driveability was really bad, so I took it to another shop and they had to make a lot of adjustments. After my Rock Jock Install they gave my jeep back to me and the tires were visibly off in a bad way and my steering wheel was a 1/4 turn off center; their computer said that the alignment was dead on

I eyeball adjusted it in my driveway with my wife's help (it was off pretty bad), and road manners improved drastically.
Anyway, Lift up each front tire about an inch individually by jacking under the axle tube. Grab the top and bottom (not the sides) of the tire and try to wiggle it back and forth. If it wiggles, you have bad wheel bearings and that is your problem. Replace em yourself (not hard), or pay a mechanic to do it. Probably not covered under warranty because of your tires.
Park on level ground. Go over top, bottom, front, and back of entire length of axle tubes with a straight edge. A bent axle tube will reveal itself. If bent, you need a new one and should be covered under warranty - or its time to upgrade
Fully inflate tires to equal pressure. On level ground, have someone spot for you while you point your tires as straight as possible. make a chalk line on the ground along the inside footprint of the tire by pushing a straight edge up against it and marking along the straight edge. Back the Jeep up and measure the distance between the fronts and backs of each chalk line. This should give you a very rough estimate of how much your alignment is off.
Ball Joints. These have to be measured with a special tool AFAIK. These go bad VERY frequently on JKs and the dealers know about it. Chrysler uses crappy ball joints that have plastic on them. The plastic rapidly wears down and problems always follow. The dealer should warranty this, but be mindful that they will replace them with the same crappy ball joints so you can do it again in a few more years. I recommend going with an all-metal ball joint like Pro-Steer instead.
Any drive-line shop / 4WP can check your pinion angle for your amount of lift in about 5 minutes. If you have a stock driveshaft, both ends must maintain almost the same angle. If you have an aftermarket double cardon shaft you can check it yourself (pinion must be in-line with shaft).
I honestly can't recommend a mechanics shop that has not overcharged me or attempted to do work that wasn't necessary - so I end up doing most of it myself. 4WP, even though not really a mechanics shop, has some knowlegable guys like Tony that may be able to help. Eds 4x4 was a good honest place, but he retired. I would PM and ask Henry who does his work, he seems to be pretty satisfied with it (I think Richard does it?). Just remember that the JK is a completely different animal than other Jeeps, so you want a mechanic who knows about them.
Good luck and let us know what you find out.