Take a look at page 25 of your owner's manual, it shows a 'blown-up' diagram.  Aside from poor milling, it looks like the only adjustment available to you is to loosen the four screws holding the motor housing and align it that way.  Otherwise, and as others have already suggested, I'd take it back.

To me that is a fairly small error in alignment.  I would wonder if a replacement would even be better?  If the lathe is otherwise perfect I would probably keep it. it would seem to be a lot of trouble to return it. Maybe correct it with Jets suggestions.  From what I read there is not a adjustment that Jet makes during assembly?  Is the bed ground on the edges so that it keeps the tail stock aligned as it moves don the bed?  Not on my NOVA, I think. 

Re reading your post.  The vibration would bother me and I would want to fix that or possibly return the lathe for vibration.  No, I do not think the alignment affects the smoothness of the lathe.  But if it vibrates while running with no workpiece there is a problem in manafacture of it.

I would spend the time to find the source of the vibration and address that with Jet.  And would try a dial indicator on the shaft.