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So don't worry so much about how to use  had had  as a unit of grammar, they will come together naturally when you want to express the verb ' to have ' in the past perfect. Let's consider a different verb for a moment like  to want .
When the subject of the that-clause is a singular pronoun such as I or he or a singular noun phrase, you can use either was or were after it. This use of were is rather formal, especially in British English. Sometimes, I wish I was back in Africa. My sister occasionally wished that she were a boy.