Shafts don't have to be in-line with each other to be parallel. You may be confusing that. The pinion shaft and transmission tailshaft on an open driveline truck that has both on the truck centerline are parallel with each other (if extended they won't intersect). They're that way so the u-joint angles are the same on both ends of the driveshaft. The same can be said for a truck that has a pinion offset from center with the engine on center. I did say that the view from the top would look just like the view from the side in the figure I posted. As long as the u-joint angles are the same on both ends and not severely angled, it should work fine. You would just have to pay attention to the u-joint angles as well as u-joint phasing.
Joe hasn't said that was the case on his truck, just that he has vibration. There are many causes of vibration.