Yes, I think that's how you would do it--measure several points objectively and draw a curve to connect them, probably hand finishing it with a file and a hammer to thin and spread out the metal if you file off too much.
If the fungus is not too bad, you may only need to have the lens cleaned. Even if there is coating damage, the lens may still be quite usable. If the lens needs to be recoated, it can be done by the manufacturer or by Focal Point Lens or Superflat. I believe that Superflat only does coating, not disassembly and reassembly.