rear tires not centered in body

First thing I would check is if the spring perches have been moved. While I'm not sure about your particular rear end, it's not uncommon for the pinion to be slightly off center by design once it's in place. I've found that on quite a few Ford 9 inchers. Someone may have moved the perches in an attempt to center the pinion in the frame before you got it. Are you sure that the wheels are not too wide even if you get everything else lined up?