past tense - when to used had been and have been

My friend just answered to one of my important questions. Now how should I reply to him?

1. That question had been in my head for a long time, finally, I got my answer

or

2. That question has been in my head for a long time, finally, I got an answer.

Basically, I am confused with had and have. Since that question is not anymore in my head after having got an answer, what should be used? (I am also confused whether it is possible to use having instead.)