So you beat the tires with a hammer to break the rust between the rim and brake?
That did not work, then you broke out the torch?
I had to do the same thing to my Indiana rust bucket.
You asked about what is a good starting point:
Mount the body on the jig. Buy a notebook. Measure everything. Write the measurements in your notebook will little sketches of the points you measured. Take more photos.
Look at your car. Make more measurments and take more photos.
A unibody is like an onion. The sheet metal is put on in layers. Examine the rockers closely. Examine the frame rails. The rockers and frame rails are the center of the onion. You will notice that the rockers are suprisingly acessible since your floor is rusted. I think the F body coupe has an inner and outer rocker. They could be replace first if needed. If the frame rails need replacing, it might be easier to cut out the floor, frame rails, and trunk pan as one big piece. Keep all the old metal. They are a perfect example how the car was constructed.
Some people cut out all the rusted parts at one time. You could do that since your car will be on a jig. I cut out one or two pieces at a time. I was afraid that if I cut too much, the car might colapse.
You are the boss. Do what you feel is best.
If you want to replace the cowl area that is good place to start. Just rememember in order to replace the cowl area the front part of the jig brace will have to be removed. The only front support will be the four subframe mounting points that might be rusted out.