Simple vs. perfect past tense

I'm writing this story from a present-tense, first person perspective, and I keep getting hung up on whether to use simple or perfect past tense when referring to something in the past. This bit in particular is tripping me up because there are so many tenses going on! Which is the better option? (To clarify, mad means crazy here, not angry.)

Part A:

1. Soldiers often return from war broken by the sins they committed for their country; is that what had happened to my mother?

2. Soldiers often return from war broken by the sins they committed for their country; is that what happened to my mother?

Part B:

1. Had she killed the witches because she was mad... or had she gone mad because she killed them?

2. Had she killed the witches because she was mad... or did she go mad because she had killed them?

3. Did she kill the witches because she was mad... or did she go mad because she had killed them?