> By "materialism" I mean that human cognition is simply an emergent property of purely physical processes in (mostly) our brains.
Again, this doesn't say what a "physical process" is, or what isn't a physical process. If "physical process" means "process", then the qualification is vacuous.
> All the individual assumptions basically come down to that same point in my view.
You're committing the fallacy of the undistributed middle. Just because both the brain and computing devices are physical, it doesn't follow that computers are capable of what the brain does. Substitute "computing devices" with "rocks".
> So either you need some magical mechanism that inserted "intelligence" at some point in our species recent evolutionary past, or an even wilder conspiracy theory (e.g. "some creator built us + current fauna exactly, and just made it look like evolution").
How intelligence came about is a separate subject, and I regrettably got sidetracked. It is irrelevant to the subject at hand. (I will say, at the risk of derailing the main discussion again, that we don't have an evolutionary explanation or any physical explanation of human intelligence. But this is a separate topic, as your main error is to assume that the physicality of intelligence entails that computation is the correct paradigm for explaining it.)
> Again, this is simply not an option if you stick to materialism in my view. you would need to assume some kind of bio-exclusive magic for this to work.
This is very difficult to address if you do not define your terms. I still don't know what matter is in your view and how intentionality fits into the picture. You can't just claim things without explanation, and "matter" is notoriously fuzzy. Try to get a physicist to define it and you'll see.
> Perceiving color is just how someones brain reacts to a stimulus? Why are you unhappy with that? What would you need from a satisfactory explanation?
I already explained that materialism suffers from issues like the problem of qualia. I took the time to give you the keywords to search for if you are not familiar with the philosophy of mind. In short, if mind is matter, and color doesn't exist in matter, then how can it exist in mind? (Again, this is tangential to the main problem with your argument.)
> Thinking, for us, results in and requires brain activity, and physically messing with our brains operation very clearly influences the whole spectrum of our cognitive capabilities, from the ability to perceive pain, color, motion, speech to consciousness itself.
I never said it doesn't involve physical activity. In fact, I even granted you, for the sake of argument, that it is entirely physical to show you the basic error you are making.
> If there was a link to something metaphysical in every persons brain, then I would expect at least some favorable indication before entertaining that notion, and I see none (or some plausible mechanism at the very least).
I don't think you know what metaphysics is. Metaphysics is not some kindof woo. It is the science of being and what must be true about reality for the observed world to be what and how it is in the most general sense. So, materialism is a metaphysical theory that claims that all that exists is matter, understood as extension in space (this is what "res extensa" refers to). But materialistic metaphysics is notoriously problematic, and I've given you one of the major problems it suffers from already (indeed, eliminativism was confected by some philosophers as a desperate attempt to save materialism from these paradoxes by making a practice out of denying observation in Procrustean fashion).