Dont really know what sort of alignment they could do anyways. The only adjustable part is the toe in and centering the steering. The toe in doesnt change with a lift, so all they would have done is centre the steering wheel and measure everything.
They should have told you the rest needs more parts replaced to fix.
I run a Rubicon Express 3in lift, about 2.5 inches front and 3in rear roughly after its settled with stock wheels (just wanted a little more ground clearance), have adjustable front trackbar (cant use a bracket on the front without flipping the draglink to keep them parallel) and a teraflex axle mounted bracket for the stock rear trackbar.
My caster is a touch under 4 degrees, really needs to be closer to 5 so has a little bumpsteer in the front but drives nicely.