Trunk Extension R&R

I pretty much had myself convinced that I was just going to replace the portion of the extension that was eaten away. Today I got the AMD replacement that I ordered and it is just too nice to not use in its entirety.
So I am looking for advice from those of you who have done this before.....what's the best approach? The quarter panel is cut away so that won't be an impediment. I am thinking that the best approach might be to cut as much of the excess away as is reasonable to that I can get at the spot welds easily. Since I will be replacing one side completely anyway, it seems like drilling all the way through the spot welds is easiest. It'll get them out of the way and then I won't have to punch any holes for the plug welds on the new steel. Make sense? I am open to all suggestions. Thanks guys. L8r