I cut out the section of the floor under the window to be replaced. Also, wire brushed and scuffed more of the surface rust off. I need to find a way to efficently clean some of those hard to reach areas...
I also started to make the replacement sheetmetal pieces to fill in the area that I cut out. Ill have to take those pictures later.
At this point I am planning on ordering a new rear quarter panel patch. This piece will mostly be used to fix that rotted out section in the door. Depending on the quality I might replace part of the quarter panel, but it is not completely necessary.