How far "off" can a chassis be?

[team39763]

Just got my new project back from the frame shop. I had a prebuilt backhalf welded on aswell as a rollbar. Took him about a year to finish it. I didn't notice anything when I picked it up(I was in a hurry, I was tired from the long drive, and a storm had hit). The next day I notice the rollbar is welded in wrong, its clearly crooked and the rear down bars are off center(by 3+ inches) and not completely welded in. That made me wonder about the frame. I talked to the builder and he said my stock frame rails weren't straight so that's why the new frame sits slightly off between the old frame rails. Does that sound right?
Anyway, I'm wondering if I can tune out any small differences in frame straightness or level with the ladder bars or shocks or Anti Roll Bar? Maybe even get a 4 wheel alignment? If I get the rear down bars redone correctly, does it matter that the main hoop is a little closer to the passenger side of the truck(maybe .5")?