Any ride height change from the Factory setting will effect alignment - toe worst, next caster, least camber. Before I started doing my own alignments at home, I would set the ride height where I wanted it ( including the rear end height ) and then take it to an alignment shop and tell them to do the alignment based on the existing ride height. Two suggestions on alignments that are often over looked. Make sure the center link is parallel to the ground. Often after market idler arms can screw this measurement up. It's one thing to have a bump steer problem. It's a hole other thing to have a bump steer problem that aint the same side to side. Try to keep the front tire / wheel offset as close to the OEM package as possible so that the scrub angle (built in to the spindle and not adjustable ) is what the OEM intended. Lastly, (I guess that's 3 things ), after you have set your front end ride height where you want it, take a look at the tie rod angles as compared to the lower control arms. They should parallel each other for minimal bump steer. The farther they are from parallel, the worse the bump steer it gonna be. With lots of front end travel, it is very difficult to satisfy this through the entire range of travel.