#1 "I was thinking" does not feel like part of your narrative. You are telling a story in which the events are: 1. I went to the kitchen and made tea 2. My husband left 3. I was thinking The third "event" doesn't feel like an event and lacks connection to the first two. If you say instead "and I started thinking" then the third item feels like an event that is connected so it feels more natural. #2 problem: There is no coherent time frame. "An hour ago" confuses the reader because nowhere is a present moment established. You can say it like this: "Early this morning I went to the kitchen and made myself a cup of tea. Waking just an hour ago NOW, I realized that my husband had left ..." Comparing the two verbs "I woke up" and "I realized", it is clear that the more important verb to your narrative is "I realized". That is why I changed "I woke up" into an adjective ("waking"). This focuses attention on the more important verb. "I woke up an hour ago" jumps the time frame, leaving the listener confused. It can be fixed by adding the single word "then": "I made a cup of tea. THEN, an hour ago I awoke and realized..." Your use of the past perfect is correct. I prefer "had gone to work" to "had left for work". The past perfect is not the only way to say what you want. You could also use "to be" instead of "to have": "I woke up and realized that my husband WAS already gone to work."

Neither 1 or 2 are clear. 1. I went down to the kitchen. Then my husband left for work and I started thinking about my own plans for the day. (You need the ‘Then’, or something similar, to clarify the timeline. ‘Was thinking’ suggests that it had been ongoing. It doesn’t fit with the story of what happened in your morning) 2. I woke up an hour ago and went down to the kitchen. I saw that my husband had already left for work. (I’m guessing that this what you meant)

Your second example is a good demonstration of the main use of the Past Perfect. We use it so that we can report past events without having to keep everything in chronological order. Before an action in the past or a point in time in the past, another action had taken place or a state had existed. He had already left before the moment when you realized that he had. The same way that the Present Perfect tells us what has happened or existed before now, the Past Perfect tells us what had happened or existed before a point in the past.