Spirit and conciousness are basically the same thing, spirit is in a sense applied conciousness. We invented the concept of conciousness to define thought or mental processes, but scientifically speaking they are just chemical reactions, complex chemical reactions, but still so nonetheless.

That being said, there aren't any fundamental phyiscal differences between a living thing, dead thing, and a thing that was never alive.

I still don't understand. Are you saying a spirit is just complex chemical reactions, going by the fact that you say spirit and conciousness are basically the same thing?

There's a fundamental physical difference between a living thing and a thing that was never alive, though. A living thing can manipulate things that were never alive, whereas it cannot happen the other way around.

The way I thought the lore worked was:

A spirit/soul is a persons personality, mindset and attitude that inhabits the body but without the spirit the body is nothing but a meatsuit basically? So like when you die your body dies but your spirit goes on forever in heaven and stuff.

That definition basically is the brain but yeah I thought that's what it was.

Conciousness does not describe the chemical reactions, it describes the human perception, the concept of self, which is what spirt boils down to at the core. There is a gap between how that translates from the chemical reactions that we observe and for all intents and purposes they might not be distinguisable.

Your second premise is not true however. Viruses are the titular example of inert material, that hijacks "living" cells to make copies of itself. Viruses are complex chains of protiens but they are not defined as living.

Living systems typically do two basic things: preserve and replicating genetic information, and maintain an organized system that decreases entropy by consuming energy and increasing entropy externally. Simply put make babies, eat, and shit. But we can and have created mechanical systems that can do these things to a degree. 

This ^

Reasons to suspect that it exists are the sighting of ghosts, pretty much, and other paranormal activity (not the movie) of the type.

No one "knows" the spirit is responsible of those functions. It is just a philosophical theory, based on faith, a belief that will, most likely, always be like that because it can't be proved or disproved. Not exclusive to religious people, btw.

This is the closest that combination of words will ever get to name something which is actually real:

The spirit inside my PC is Windows 7. The spirit inside my MacBook is OS X Yosemite. The ghost in the machine is the instructions that make you the way you are.

Party members' stat that increases Magic Defense.

About 21 grams

But you just said scientifically speaking, thought or mental processes, which is what we define conciousness by, is just complex chemical reactions. You also said spirit and conciousness is basically the same thing (one being the applied of the other); hence the conclusion of spirit = complex chemical reaction. As for the other thing, ff the gap might not be distinguisable, how could you argue that there's a gap in the first place?

As for this, I lack the knowledge to fully support the living thing claim, so I won't try to argue back here, even though I have the feeling that viruses are just the unexplicable exception to the rule I proposed earlier.

The second premise points at those mechanical system, but why would those mechanical systems do those things unless they were programmed to? Again, a living thing manipulating something that was never living in the first place. Just because you can construct something that is supposed to replicate what living things does doesn't make it a living thing. Why would a machine want to replicate its genetic information? If such construct would exist, then I'd need to investigate deeper, though you could make a claim that those never living things are actually the same as living things; but then again, (and not to go further from what I claimed toward OP's question) when such machine cease to exist, there's nothing left for it. There's no robotic spirit, no robotic trascendence. It would simply turn off, just like living things cease to live.