Even when I am replacing just small pieces of a panel or floorboard, I always purchase the aftermarket panels and cut what I need out of them. Reason being, they have the proper stamped areas that you can't easily duplicate. The floor panels are relatively easy. Its when you get into the toeboard or inside cowl that things get interesting.
Others will argue that the aftermarket floor panels aren't the same gauge as original, but unless you have a donor cab with good floorboards, its the next best thing. In the end, its not possible to tell the difference if done right.