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Dear C E,
I would leave the window alone. Aluminum windows are typically electro statically painted in a controlled environment when they were originally built at the factory. This environment includes air cleaners, pressure sprayers, heat/infrared curing ovens and lots of air handling equipment (large fans). This controlled environment leaves your aluminum windows looking like brand new car paint finishes. It is nearly impossible to replicate such an environment in the field at your home thus leaving many people with unhappy results when they try to repaint aluminum windows after they have been installed. The weather effects and pitting you describe make this process almost impossible. I believe you will be in for a lot of work and frustration and not happy with your end result if you try such a task.
Sincerely,
John Patrick
President, Larmco Windows, Inc.