Mike, It would be best to do the floor one side at a time to keep things from running away on you.
When replacing the cowl panels, I learned that using little self-tapping hex-head screws saves the day when it comes to final fitment later, especially at the hinge pillars. Its a lot easier to remove some screws rather than grinding out welds. Once everything fits right, remove a screw at a time, drill the outermost panel, then weld the panel to the underlying panel.
Carl
