1-1. Jane said to Jim, "I didn't tell your mother anything about what you [did, had done] to Peter."
Either tense is OK, but "did" is more likely.
1-2. Jane told Jim that she hadn't told his mother anything about what he [did, had done] to Peter.
Either tense is OK but "did" is more likely.
2-1. His secretary said to him, "there were no phone calls while you were out."
2-2. His secretary told him that there had been no phone calls while he [was, had been] out.
Both are theoretically correct, but "was" is overwhelmingly more natural than "had been."