Removing & installing new frame

wow sounds like a huge undertaking.
It would help if you have access to a FSM or a frame shop with specs for the frame measurements, if not I would say measure the "keeper" car at the respective alignment holes in relation to the rest of the frame ( key points ) and weld the new panel in exactly the same place. You don't want to line it all up and have the thing drive like it's got 4 wheel steering only to find that the shop says "the frame is straight" because you "made" the frame straight when you welded it in..
I've heard of guys adding more spot welds or welding the seams on a unibody to make them a little more rigid... but I've never seen/done it myself.