UPDATE: It looks like there are 2 things at play here.

1. somehow my fender on the passenger side is nearly 2 inches further back (towards the glass) than the driver side is.. this is why the fender rubs. using the tubular arms the shop measured everything and the subframe looks within spec. his machine thinks the alignment is good. for now i am just going to roll the fender enough to drive it.

2. the steering not returning to center, i was told is most likely the worm gear in the steering box. he said due to it being a rebuilt box they are known to crank down on the worm gears when they replace them and they have to wear in.. not sure I'm buying into that as things were pretty tight without the steering box connected but ill give it a shot.