past perfect vs simple past

Pepper and I had done everything together. We played, slept and ate in synchrony, but most importantly, we understood each other without ever having shared a conversation. My canine friend taught me how to communicate without using words and instead by observing the needs of others. I attribute my keen ability to emotionally connect with people, sometimes without words, to her. It was this ability that I called upon when I first began working with non-verbal, developmentally delayed children. It was critical that I understood their non-verbal behavior in order to facilitate their communicative capabilities.

What had just happened? That was what I had thought to myself as I ran down the hall after my student while simultaneously pressing the timer and documenting his escapement. The speech pathologist and I had lost our student’s attention while we were pairing his preferred phoneme of /u/ with his favorite activity of blowing bubbles. As the student and I developed a relationship I had begun to understand his personality, limits and preferences, which enabled me to implement child-centered lessons that were both educational and fun.

I am not sure if I have used the correct tenses (i.e.,past perfect vs simple past)