Trying to match the cut lines of two distinct large panels is almost impossible. The best way to accomplish a best result for welding is to lay the new skin over your existing quarter. Align the skin from bottom and work you way up. Once you are satisfied with fit, anchor the skin to existing quarter with a just few small diameter sheet metal screws or Cleco fasteners above & outside where you want the panels to butt up. You can use the outer wheelhouse and trunk drop off panel as lower anchor surfaces. Once completely anchored, scribe a cut line on the new skin. Then cut through both panels with a thin cut off wheel (<=1/16") along the cut line. Once cut, both panels will be pretty much matched with a good weldable gap all the way around.
There's quite a few videos on YouTube that demonstrate the technique. I strongly suggest reviewing as many as you can.
Good luck!