There is a bit for me to unpack, but I will do my best.
BA - Quite right, it isn't established that Ghosts are a byproduct of the soul. At least, not stated explicitly. But it is stated that ghosts are the footprint and the water that fills it (on the hypothetical beach), not the foot. So I think that Jim has at least inferred it. What isn't clear is whether souless beings can have "ghosts" like mortals. I don't believe so based on the fact the mortals are a soul, but have a body. We haven't yet seen the ghost of an immortal, although it is theorized a Demon could leave a ghost. Perhaps the Dinosaurs did have souls. Who knows? I would say when it comes to animals though, it is merely the magical part of the being that all physical beings seem to have. I have yet to see a being in the Dresden Files that has no "shadow" in the spiritual world (that is to say, entirely untouched by magic).
As for the "Death of the Author"...it was a literary essay, and one that didn't escape critiscm. Whilst it is perhaps used as a lens it isn't an objective truth. It might contain elements of truth, but that isn't the same thing. You can use it if you wish, I won't stop you. But as far as I am concerned if we are discussing theory we all have to share a basic set of rules. If we all just get to decide which rules apply and which don't because we are all special snowflakes it rather defeats the purpose of these discussions. How can any argument be presented if we can't even agree on what the facts are? How can we develop a strong theory, too? Alternative facts, are in my opinion, a lazy mind's excuse for not using critical thinking. Why even read the books if you don't accept what is in them? Might as well write your own and make another forum to go with it.
Morris - I should hope not, I rather enjoy our chats. As I do with just about everyone on here. You are of course, correct. Subtext, intention, inference and implication are the stuff that get people going. It would make for a dull series without it. And how our experiences as people meld with the story is what allow us to connect with it, hence the payoff. I would never argue to get rid of that. And I agree, we do have to agree on a shared reality. But we aren't agreeing, this whole forum often doesn't. And nor should it. But in order to have a coherent discussion that isn't derailed all the time, we have to agree on basic tenets. One of which is that if it is written in the novels, or said in a WOJ etc, that's the gospel. If it is disagreed with, or thought to be false, appropriate evidence must be applied to support that position. We cannot simply argue that for example, "Harry is actually a god in Storm Front because I believe it to be so, and that works for me". Obviously, that assertion is ridiculous and has no text or statement outside the series to support it. So I would have to gather evidence to support the argument - subtext, inference, literary devices, examples etc. Without the evidence to debate there is nothing for anyone to work with. We could flood the forums with crack theories with absolutely no basis in reality for the sole purpose of our own peverse pleasure. The boards are a community, a shared space, and so should be treated with the respect that deserves. No one here stands above the rest (although Griffyn does run the place) but even his theories don't carry more weight because of that. Not having a go at you in particular either. Just giving my two bob.
Jim doesn't have to provide all the markers. We can deduce much ourselves. And he may have further reveals that he is saving up. Whilst I agree on much of the soul/spirit thing being interchangeable...there are some inconsitencies. And yes, there are differences. Were the Sir Stuart we met merely a ghost or spectre, he is but the shadow of the real deal. The real Sir Stuart is in the Here After and both are experiencing reality differently. If this were a sci-fi novel, and you replace ghost with "clone", let's say the clone has all the memories of the original being but once it is created does it's own thing, has it's own experiences. It stops being the first being just by having different experiences. It becomes something else. However, if Sir Stuart is actually more than a mere ghost - he is also a soul that is called Sir Stuart AND his ghost self then he isn't so different from Harry. Depends which theory you believe.
The Archive doesn't manifest, it has a vessel. No more than a computer program has relevance or manifests outside the paradigm of cyber. As for the others...Bob and Evil Bob have yet to create physical bodies, they have so far either possessed physical beings or interacted on different level of reality. Bonnie is something different again but I won't get into that now.