Pumice stones work sometimes. Another option would be to buy an acid based commercial toilet bowl cleaner from a local janitorial company. If you don't know where to find one call local motels and ask. However unless you fix the iron problem it will just come back. New toilets can be as cheap as $40 but again the stains will return. I have my own well water also and have high levels of iron from the cast iron casing corrosion from naturally high levels of calcium and magnesium in the water. Most softeners can only reduce iron levels up to 5ppm. Additional filtration may be required. A more costly fix could be to reline your well with modern plastic casing if it isn't already.
High iron levels quite often lead to "rotten egg" smell in your hot water heater from sulfite bacteria.