Rear frame bent?

Definitely center your axle on the springs. Perches must be equidistant from center of axle housing. All other considerations are secondary. I feel your pain to a degree, after mini tub, spring relocation, and diff shortening I found a 3/8" difference between left and right fender which was not in the mini tub work but actually in the distance between frame rail and outer edge of fender lip. Had I known this was typical for the era, I could have accounted for a portion of this by shortening the rear less on each side.