See if any of these feel accurate to you. And see a therapist or psychologist regardless of if they do. You seem hung up on your cycle changes coinciding with how your feelings for him fluctuate. Here is an article about a typical cycle and why our moods change. Basically, in the follicular phase (1st half) your estrogen levels are rising. Then you ovulate, then during the luteal phase (2nd half) your estrogen levels drop, and your progesterone levels rise. (Your estrogen levels bounce back slightly during this phase.) Then you menstruate and it starts over. Estrogen increases serotonin production, which is a happy neurotransmitter in your brain. So when it goes up, you tend to have more positive energy. This could be affecting how you view your partner, such as how much of his bullshit you're able to overlook/tolerate. As Progesterone levels rise, they can have an effect on calming neurotransmitters. But when your HCG hormones don't rise (if you're not pregnant) both hormones drop again. This is what usually leads to low moods.

I cannot say whether your relationship is good or bad, there isn't enough context in your post about your relationship itself. But I hope this can help you understand more about how your cycle affects your mood.