1. David had been married to her for five years by then.
2. David has been married to her for five years by then.
1. David had been married to her for five years by then . 2.
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1. David had been married to her for five years by then.
2. David has been married to her for five years by then.
Only 1. is correct. The past perfect is required because their marriage of five years is anterior to some date that is the antecedent of "then".