Where does the soul reside? A rationalist analysis

In the recent debates about whether brain death should be counted as death in terms of organ donation, an interesting side debate occurred regarding the soul. The question is, where does the soul reside? Someone proposed that it cannot reside in the arm, because if someone loses their arm, they haven't lost their soul. Likewise for all other organs of their body, except the brain, ergo the soul must reside in the brain. However, I think this logic is not very rational at all. Firstly, the soul lives on the spiritual, non physical plain. Therefore, the soul's connection to the physical plain is clearly not at the physical level, this would be an irrational contradiction in terms. Secondly, it could be that the soul does generally reside in the arm, but if the arm gets cut off, then the soul takes up residence in another part of the anatomy. I guess the brain is a last resort, but only because the person is still living while they have a brain, not because the soul likes to reside there. Certainly, souls don't like to reside in dead bodies, for obvious reasons. Now, souls are immortal, as otherwise there wouldn't be much point to them. Once a soul leaves a body, it becomes disembodied (by definition) and goes up to heaven. It might then come back to earth again to inhabit a different body. This seems quite rational (assuming souls exist in the first place). A multi body soul would be quite an interesting person, I mean soul. But most of this is besides the point. I think that Chareidim, and indeed all Orthodox Jewish fundamentalists, are forced to hold that the brain-dead are not truly dead, as otherwise, we could never make a minyan. Badaboom.

But seriously, I do have a point. Most of the arguments in this debate are erroneous. "Death" in halachah is a halachic state. As someone on a blog noted, we could call it "meis" instead. So who is a meis? Whomever Chazal / Gedolim / Your Local Rabbi says is a meis.

Considering that nobody 2,000 years ago had any clue of modern science, (nor would such knowledge make much difference back then given the absence of modern medical technology), any halachah from 2,000 years ago is bound not to jive with modern medical ethics.

Likewise ancient values from 2,000 years ago (e.g. attitudes towards women, blood, homosexuality etc) are not going to jive with modern values, at least not without a lot of kvetching. I suppose you could say it all comes from God, and God designed the system very wisely, to apply for all times, but then that wouldn't be very rational, would it? There's also no rational reason to suppose that the halachic "process", as defined 2,000-1,000 years ago, is a good "process" that will always get at the "truth" (or rather a verdict consonant with modern technology and/or ethics).

If the value of halachah is greater than the sum of its parts (e.g. meaning, membership in an exclusive club, relief from guilt etc), and/or the reason to hold of halachah is that it came from God, then what is the motivation to be so rational about it? What is the motivation to assume that Chazal must have been wrong about death? Maybe Chazal were right about death halachah (without a good rational reason to think so), just like they were "right" to believe that God wrote the Torah, even though from a truly rational perspective that's a bunch of bs.

It appears that the real motivation here is to ensure that halachah conforms to modern notions of ethics, morals and of course science. From a truly rational perspective, this is very admirable. However from a religious fundamentalist perspective, it strikes at the heart (err I mean brain?) of the entire religious enterprise. Life and death are fundamental religious concepts, if their definition is left to the scientists, then who needs Rabbis? (Speaking metaphorically).