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Stock JK TechBulletin board forum regarding issues with OE (original equipment) components of the Jeep JK Wrangler (Rubicon, Sahara, Unlimited and X) such as factory suspension parts, engine, transmission, body parts, interior fixtures and the on-board computer.
After you get her cleaned up keep up on applying an acrylic sealant and a wax. It'll prevent the rust spots from adhering to the paint and will wash off with a normal car wash.