' had become' is correct as past perfect is used to refer an action which got over before the other began. with regard to the second one, 'will have cleaned' is correct as it denotes the completion of the action before you get home. And for the same reason, had died is correct in the second sentence.
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AnonymousWhat's the exact meaning of 'by the time'? Is it 'before'?Yes. Roughly, 'before'. There is the added implication of "any time before, but definitely not after".