shocks dont have anything to do with it.
Did you get a printout of your specs from the shop that did the "Alignment". It sounds like you are talking about camber, which is not adjustable from the factory on our trucks. You have to get a "camber kit", which isn't a huge deal, they should have told you if it was an issue. It is possible the torsion crank threw your camber off. Many MANY shops just set the Toe on the cars (hell even some by eye) and let the car go if it doesn't pull or anything...which is why they may not have even mentioned it.
JK Rubicon, 2dr - 37s, beadlocks, ram assist, cage, 12klb winch, etc, etc