so if i'm hearing you correctly, I should be adjusting the panhard bar to center the rear wheels relative to the front wheels and not the actual frame of the car? have others seen this issue ?Chewy: I also use the string method. Once you have "strung" both sides, make sure the string is the same height from the ground on both sides of the car all along the side, ie front, middle and rear are all the same, and that the string is at the center of the wheel. I like to measure at the rim of the wheel (after all that is where the alignment heads attach on a real alignment machine). Using the side wall may introduce variances, and exaggerate your true toe.
I also found a difference in measurement side to side as you did, indicating the rear is off to one side. I adjusted the panhard bar to make sure the distance from front wheels to string is the same both sides. You are only off less that 1/2 inch side to side. Measuring from the shock towers is probably not accurate...they are welded in place by a human! I would center the rear, or "square" it, relative to the front, and proceed from there.
Others may have other input, and I welcome any suggestions.