Most times when you do an engine swap, the engine will be offset to the passenger side by some amount. . . the amount depending on the size of the replacement engine. Most people don't realize that many factory engines are also offset. Another thing people don't realize is that the pinion center line in hardly ever on the center line of the frame. They, also are offset to the passenger side. It doesn't matter that the two U-joints are not on the same centerline from the front of the frame to the back (my engine is set right 2" and the pinion is 1-1/2" right.) It only matters that their individual centerlines are parallel.. Answered my own question I think.
Just freaked me out for a few.