"Ha, red herring now! ie., not answering the question."

I thought my response did answer your question. Please read your question and my response again, and let me know what I have failed to answer.

"The brain understands all that and takes it into account as it produces thoughts about itself in the world. The brain is the locus of mental life, but it isn’t mental life. Just as the lungs are the locus of respiration, but the lungs are not respiration."

But the lungs do the breathing, just as the brain thinks the thoughts. Without the lungs, no breathing. Without a brain, no thoughts. And since the brain is altered by our experiences, and we don't have control over all our experiences, we don't have free choice over our thoughts. You are not free to think a thought it doesn't occur to you to think. You are not free to choose something you are not aware is a choice.

"I can have mental understanding of the effect of my brain on my mental understanding then go in and change my brain to change my understanding; for one example, by CHOOSING to take or not to take an anti-depressant, or to take up meditation instead."

You will choose whether to take an anti-depressant or take up meditation based on various factors, such as what has worked for you in the past, what has worked for other people you know, what your doctor says, what the research says, etc. You could say you choose whether to go in search that information and whether to pay attention to it. But whether you do or not will also be based on prior factors you did not choose.

You are also not consciously aware of everything your brain is doing right now.

"My mental states include understandings of what causes my mental states, and I then choose to alter that relative to…to what?"

There's no way we can know every factor that affects our brains. That would be impossible because it would mean being aware of everything that is related to us in some way.

"Is the brain determined by the brain to choose to alter itself?"

What do you mean? The brain is how it is at any given moment, but is altered by life experiences.

"What is the "I" that chooses to alter my own brain?"

There isn't one.

"Or, our mental life includes self-conscious (abstract) understandings of itself (including the brain) and can then take that understanding into account as it chooses to do x, y, or z."

The brains ability to do that is limited by the brain's state at that moment, which the brain did not choose.