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To really do it right, any pitting in the tubes, spring perches, shock brackets, etc, should be filled with plastic, so you don't get that painted rust pit look. If you fill the pitting, it has to be painted, cause the filler can't be powder coated.
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The powder coater I used recently would not coat any of the parts I had unless ALL the paint had been stripped off the parts I wanted done. I had them chemically stripped before took them back to him. This contradicts what happened in your case.
Martin