Thanks Seth! Sorry for the late response, I haven't had time to update for a few days so now it's catch up time...
Here is my plan to repair the rusted flange for the inner fender wall. Being that it was all rotted out I cut the whole thing off to make the repair simpler.
This is what's left of the inner wall. I cut the rusty wiring channel off right at the bottom of the wall.

After cleaning up the sheet metal I will make a new "J" channel to plug weld to the old inner wall.
This is my "plan" sketched out on that same pic. The black is the new channel, the blue is the new inner rocker.

Here is a hand drawn pic of the assembly before cutting off the flange.

With the new flange plug welded in and the rocker/floor relationship.

I will build this assembly with screws and Cleco's before anything gets welded in.
Tonight I will get rest of the inner rocker removed and start CLEANING all of the rust and junk out... I also have some patching to do on the outer so that will get done before I do the inner.
Mark