the shaft there, it only fits one way, dont affect the alignment. what i do is pull the shaft down as far as it will go, then jack the frame up to the shaft till it like a inch or two pushing the shaft back up, then work on getting it back on the rack nub.
once you got the wheels back on and its on the ground you can reach around the tire and turn the inner rod to adjust the toe in/out enough to get you to shop.