Yuppers ,same thing i went through, did you loosen the 2 nuts on the frame side of the lower control arms so the bolt would come out ?
To get stuff to line back up i used a come along if i remember , not the best but it worked ok. To get the control arm to line up,put the top in and then have someone turn the sterring wheel till the bolt on the axle end lines up. should be 3 quarters of an inch longer than the stock track bar.
How come you messed with the brake lines ? just straiten out the stock ones at the frame and that should do it,have to redrill the hole lower is all for the self tap bolt.
Are the upper and lower control arms the same length as stock ? The pitman arm is off the box isnt it ?
Hope i dont screw you up here,kinda tired tonight,,,,,,,,still !! working on mine ,a few bugs here and there,oh ya and over there,,shit