I say clean to see what you really have. If you have a sandblaster that would be better. The rocker panels are a must replace from looking at the photos so you don't have to clean them. Once it is clean mount it back to the frame and replace a piece at a time, for all the reasons mentioned above. There seems to me to be a lot of good metal left under the seat pan. You can make some of the replacement parts out of sheet metal. I made some of the inner panels on the cowl and cab corners.
http://rides.webshots.com/album/563027192ItmeAM?start=72 You could probably make the floor behind the seat patch. I like the idea of saving one that is on the ragged edge of to far gone. Mine was every bit as bad but it is looking better all the time.