I am in the process of repairing similar damage to my floor board and toe boards. I have also looked at how others have suggested doing it. A couple things to think about. If you replace the floor panels and and accompanying cab mounts in place you match cab to frame. I looked at this and believe if it is done while the cab is off that you will have to use additional supports. I didn't want to take a chance on this so I have replaced the panels before pulling my cab(1950 3600). I used the cab mount hardware (new) to help assure the panels were correctly fitted. My plan is once all the major work on the floor is complete to pull it and finish the additional work. I have also stripped and rebuilt my doors and hinges so they come off and on easily (lots of work so something to think about).
I also completely rebuilt my bed and the easiest way to store it is to dissasemble it since you are replacing most of it anyway. Then the pieces lay flat and you can work on them individually (I used metal sawhorses). I replaced my front panel, two sills, and rear stake pockets. This work is really easy to do with the bed in pieces. Here is my work so far if you have any other questions drop me a line.
http://community.webshots.com/user/RugerWSM?vhost=community 
