See, Ballin, these are good questions. Even when I see things differently than you, I feel like it's a productive conversation. Let's go through some things:
First is that we have to be wary of an infinite regress of definitions. No matter what I answer, you can always come back and say "well what does THAT mean?". If you're expecting a complete universal Theory of Everything, I'm going to leave you disappointed.
So I think it's pretty clear what is meant by "caused". It's a specific interaction which is governed by the laws of nature. Our best view into them thus far is quantum mechanics. Essentially says things like "If particle X travels at particle Y with such and such properties, Z happens". Conditions are set and determined, then an effect is produced. Cause and effect.
What are the fundamental constituents of the universe? Another good question. The obvious answer is that we don't know with a whole lot of certainty. At a certain level, all the "particles" wind up not being particles at all, but rather probability distribution fields. IE: Basic mathematical constructs. As if the world is only made of math, and that all macroscopic phenomenon are emergent behaviors from this. Fascinating stuff. But not ultimately important for us. Whatever it is that's actually the fundamental constituent of the universe, that's what causality applies to directly.
How do you know causality pertains only to fundamental constituents of the universe? See? Another great question! This one is easy if you think about it for a moment. Whatever this particle (for the sake of being being concise) is, that's all there exists in the universe. All of existence is a huge soup of this stuff. There is nothing else.
These particles sometimes arrange themselves into unique patterns and shapes, which we then give names like "molecules". But the molecule is an illusion. Really all that exists is that fundamental particle. So it's not that "causality only applies to the fundamental constituent". It's that "ALL laws only apply to that particle". (Since that particle is the only thing which really exists)
"Also, it seems like you are rejecting action at a distance". Yes I am. This is called the Principle of Locality. I will note that not every interpretation of Quantum Mechanics relies on Locality. There are some consistent theories which include non-locality. Put more rigorously: "Experiments have shown that quantum mechanically entangled particles must violate either the principle of locality or the form of philosophical realism known as counterfactual definiteness"
The Copenhagen Interpretation is by far the most adhered to, and involves maintaining Locality. But this isn't very important for us.
But I'll ask this question: why did I think of Paris, togas, and chopsticks just now? What caused these thoughts?
The brain is wildly complex, so of course you don't expect me to give you a complete biochemical account of precisely how those specific thoughts came about in your head. But that's not important. My point is merely that those thoughts happened entirely within your head. And that your head is governed by the same laws of nature that rocks are. Which is to say that your head doesn't get special treatment.
A thought is a process within the mind. The mind may be a product of the brain, in the sense that all minds are associated with brains, but it's easy to show that they aren't the same thing. You can imagine a mind existing without any brain. This proves that they aren't the same concept.
Careful with your wording here. The brain and the mind are different CONCEPTS. Yes. That does not prove that there exists a mind separate from the body. One can imagine a bodiless mind, sure.
One can also imagine many things which don't exist. Imagining it doesn't make it real. I'm not saying it's inconceivable for there to be bodiless minds, I'm saying that they're not real. (More specifically, that they contradict all of science)
This isn't true though. Because how do we know what we know about modern science and the way the universe works? By studying non-human objects. In fact, our knowledge of the mind is more fundamental than our knowledge of other objects (see Descartes' Meditations). I don't see how that is appealing to anything supernatural.
I've been very careful with my wording here. I've refrained from calling Free Will fully impossible on purpose. If you're keen on just rejecting all scientific discoveries and theories, then sure, go ahead and have your Free Will. But don't expect anyone to take you seriously.
You may really want 1=2 to be true. And so you reject all of mathematics for it to be true. Sure. But that's not a terribly compelling argument.
A Flat Earth is more likely than Free Will. In order for a Flat Earth to be true, it would require a complete upheaval of astrophysics, combined with a massive conspiracy theory. But at least parts of it are otherwise plausible. Free Will just breaks everything, and I mean everything.
EDIT: I will say that Free Will has one thing going for it: It undoubtedly FEELS like we have it. But I think that anyone here can see that this is hardly an argument at all. Intuition is an evolutionary product forged under the context of ordinary earthly experience. It is not at all to be trusted in matters of science.