aha;
the bridge notches actually look right, it's the neck that's crooked!
you need to loosen the three neck screws, then push the neck over towards the treble side until the outer strings both line up with the edges of the neck, then re-tighten
I get what you're saying, however I can't even fit a .0015" feeler gauge between neck and body.
If the neck could be moved to the right, wouldn't that exacerbate the alignment of the E in the saddle?
Something that just occurred to me is I don't recall the original string specs. Could it be that fitting thicker strings after setup by a luthier would cause such an issue?