If you're going to doing major surgery on the floor boards and sills I'd strongly advise against pulling the body until you get the parts tacked in and you've verified that the doors are fit properly AND the holes in the floor line up with the pedals and steering column.
After that was done, I'd pull the body... and still, that's a lot of flexible steel to be moving around separated from critical alignment points to the frame and trying to guess where braces should go is a crap shoot. Trust me, you'd be amazed at how much things move once they're disassembled.
