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There really isn't much you can do to fix rust spots. Usually the entire panel will need to be sanded and repainted but even then there is still a chance that the rust will return within a few years or even months.
Mine had the old metal cut out,new metal welded in,yet the rust will ALWAYS come back.OInce you get it,it`s there for good,and i don`t drive my SHO from October until May.
The reason why rust is so hard to get rid of is that the new metal that is welded back in usually does not have the same rust restant coatings applied and/or the coatings are damaged when the panels are welded. If you are carful to completly coat the inside of any patches you make with POR 15 or some other rustproofing you should a long lasting patch.