It seems pretty impossible that acid rain was the cause of your problems. Did the contractor purposely spray acid rain out of his hose? Unfortunately, aluminum siding does fade over time and becomes chalky, so washing it can produce some ugly outcomes. Depending on the size of your house, it shouldn't cost too much to paint it. If it's never been painted before, you don't have to prime. You only have to apply two-three coats of 100% acrylic latex paint (I prefer Benjamin Moore). If your siding still feels chalky, there is a paint additive that will help your paint stick better. Good luck!