Good luck getting your car aligned as it sits, I know I wouldn't touch it. I don't think with it lowered and the body kit that a laser alignment machine can even read the car. I dunno about the new 3D machines though.

And yes, check your brake pads, make sure they're installed properly and make sure the caliper pins are clean and greased up with fresh graphite grease. Also make sure the saddles are clean and free of brake dust. Than re-test and see if the problem corrects. If not, re-bleed the lines.