Another thing to remember, and keep track of during the whole process, is that the origional panel is not flat, but has a slight curve to it, and that curve will "suck in" when you make a cut longitudinally.
With nothing behind it to hold it in the proper position when the new panel is welded in you get what you have there. But you can cut your tacks, and get the panel in proper alignment, and sew it up.
I've actually gone so far as to make a few templates out of sheet metal to hold the parts in proper alignment. And when done, I put them on the shelf, for future use. I had a few different sets made for the 55 chevy 1/4 panel, Model A door, and '65 chevy pickup bed side.