Your last photo shows the rocker rusted away from the A pillar, which would explain why the rear of the cab is listing to the right. You'll need to fix that.
Your plan on putting new sheet metal over the rusted stuff isn't a good one. You'll find that it won't work well. You should really cut away the rusted panel and weld the new panels in place. As an example, if you take two hemispheres of the same diameter, they won't nest exactly because of the thickness of the material. If you don't have a Factory Assembly Manual, you should get one and refer to the cab welding dimensions shown on Section 1, Sheet 1.07. You should get the floor and rocker in the right location reference to the door hinge bolts on the A pillar.
You'll also find that most repair panels aren't a perfect fit and will need trimming, bending, etc.
I've been through this. You can look at the photo link in my signature and follow along.
