I suspect that doing it a little bit at a time may very well end up taking you longer but it probably can be done the way you suggest. The side panels are relatively stiff but you may be able to flex them out of the way enough if you take out the rivets most of the way up to the top edge. If you do that though it would not be that much harder to just take them all the way out. Taking the panels out and putting them back in is not really all that hard compared to removing and replacing the floor itself. On my 31' AS there are only about 3 pieces total along the lower row on the sides that I had to take out. The really long pieces can be rolled up and taped or tied for storage if you don't have room for them flat. There really are not all that many rivets involved. Also depending on what year your AS is you might find that there are 5/8" plywood splices under the edges of the sheets of plywood at the joints between sheets. You can not fully remove these until both sheets of plywood that sit on them are removed.
The bracing technique that I used is really pretty easy to implement and does not take very much material. Again it is easier to install the bracing than to remove the flooring. I guess my oppinion is that you would be better off doing each of the steps all at once rather than trying to do it piece meal. You will find that there is a lot less setup and take down of your tools and welding equiptment too.
I found that I needed a combination of different tools to get the floor pieces out. There is more detail in some of the postings that I mention below but let me summarize here:
1.) A circular saw is a good choice for cutting the majority of the plywood out. I set the saw blade depth to just under the thickness of the plywood. I then marked and cut out the center sections of each plywood sheet along the edges of the cross members and as near to the sides of the body as I could conveniently get. The objective here is to end up with narrow strips of wood on top of the frame cross-members and around the edges of the body. Once you cut the pieces you can pry them out with a slim crow bar. If the belly pan is off you can hit them from underneath with a hammer to break loose the tiny bit of plywood that your circular saw did not cut. With the saw blade set to the correct depth you will not cut into the frame and you just need to avoid the screw and bolts where the plywood is attached to the cross memebers.
2.) A sazall (or reciprocating saw) is very helpfull for cutting through the bolts that hold the plywood strips to the cross-members. I used a pry bar to help lift the plywood off of the frame a bit so the saw would not bind so much on the wood when you cut the bolts. Cut them between the wood and the top of the frame. In my case there were replacement screws on some of the floor that must have been stainless steel. They were very hard to saw with a normal metal cutting blade. I used an abrasive blade instead and had better results. I did not use my recip saw very much around the edges for fear of cutting into the outer body panels.
3.) Some type of cutoff wheel to help cut the screws and bolts around the bottom of the body. I have an air powered one but a roto-zip or a dremel tool can work. You will use a lot of blades with the dremel since they are a bit small for the task.
4.) Hand hack saw - the type with a handle that the blade sticks out from. I found there were a few places where I found it easier to just carefully saw a bolt or screw by hand. The saw I bought had a terrible blade to start with by the way. Once I replaced it with a good one the work was a lot easier.
I am sure that you have seen at least some of the following threads but I mention them again for others too:
An alternative to plywood
Some discussion about shell on techniques.
"Shell Off vs Shell On
" several notes especially my post #74
"HELP!!! On a tight schedule, need to replace...
" my post #26
The best thing to do is to take your time and think through each of the steps. If you run into any specific snags I would be happy to try to help as much as I can. For what its worth I do have the dubious distinction of being one of the few people (if not the only one) who has replaced their floor twice in the same remodeling session.