When I did my door jamb repair I did it as I fit the doors. That is an area as you can see which has a lot of lead in it:
http://www.rc-tech.net/pantera1/door/door.htm
When I did some of my frame repair I also added support in some areas with notches and drain holes to ensure the areas still drain:


I also welded in some panels which helped clean up the look of the rear trunk:
http://www.rc-tech.net/pantera1/paint2/well.jpg
http://www.rc-tech.net/pantera1/paint2/wc2.jpg
http://www.rc-tech.net/pantera1/paint2/well6.jpg
http://www.rc-tech.net/pantera1/paint1/tub2.jpg
On the rear tail I added a plate to make sure it is a solid area which would not be damaged if I wanted to jack there:

Just some ideas
Gary