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As to what would cost the most... depends on how much rust you have there... but I am guessing repairing the rust will cost more... unless the leaks are serious and related to the heads and not some valve cover gasket, oil line...
in the door jam below the rubber moulding is common,also is below the windsheild. if its a small spot it sanded lightly and can be treated with Krylon rust stopper then touched up.I havent heard of the other location your talking about in the side back window.hope that helps.