That rust stain on the top tube is from the cable clamp. Simplex clamps are not stainless steel like Campagnolo. The chrome cracks from bending them and they rust. Rub it out with some white rubbing compound. New Simplex clamps can be found on eBay.
Your bridge wire rubs the seat tubes because your hanger is angled incorrectly.
The rust in the BB shell is insignificant. Use some kind of rust remover if it will make you feel better. Otherwise, it may rust out in about 200 years.