It might be me but I don't understand most of that?
What is a 9"? You mean you want to put a Ford axle in the car?
What has that to do with rust in the chassis?
Also this bit about "how much can I cut out"? How much of what cut out of what and why?
I am just a slow Northerner you know? You have to talk slow for me to understand.
The bits I did understand are that the chassis has some rot in it. Maybe the floorpan too?
Auto Rust Technicians sell chassis repair sections. You can get replacement floor panels from several sources. The chassis torque box sections that were fitted to the 440/426 and convertibles can be bought from them too and they add a far bit of strength.
As for chassis connectors. Always a good thing. I would use them on anything other than a proper restoration and any car that sees the strip wearing sticky tires or slicks.
Roll cage. Fit one if you want but if your car runs 13s or slower you might get laughed at. If it runs mid 11s or faster you need one for sure. Roll cage is optional between those power levels.
Hope that helps.
And please tell me you are not fitting a Ford axle?