remember - surface rust can be dealt with, rust holes can be repaired, but rot is rot and that has to be replaced.
A perfect example is the '69 that Chris Fesler bought from Tyler's client. It really was a solid car...but had some rust so Chris did patches on it...that way he was able to keep all the OE panels (they fit nice!) and the metal work didn't spiral out of control. Once you really tare into a car and start replacing many panels you are talking a lot of metal work...and then comes the huge hours of fitting sheet metal and body work! Todd's car is also a great example of patshing the bad areas and moving on.
I would clean up the metal and see what you really have. Surface rust is very common so don't freak out. Patches can be done and if done correctly are undetectable. On my floor I had a few pin holes that I welded up and one small patch that I had to do on the floor...deffinatly wasn't worth cutting the floor out.
Let us know what you have once you dig a little deeper!!