1
1) had had
2) had done
3) had stopped
4) had missed
5) had written
2
1) had done; phoned
2) repaired; had come
3) had visited
4) entered; understood; had been
5) had written; went
3
1) I had done my homework.
2) I repaired my computer.
3) I had trained.
4) I had found it.
5) I had woken up.