Another not-speaking-for-LW answer:

Re #1: I certainly agree that we experience things, and that therefore the causes of our experience exist. I don't really care what name we attach to those causes... what matters is the thing and how it relates to other things, not the label. That said, in general I think the label "qualia" causes more trouble due to conceptual baggage than it resolves, much like the label "soul".

Re #2: This argument is oversimplistic, but I find the conclusion likely.
More precisely: there are things outside my brain (like, say, my adrenal glands or my testicles) that alter certain aspects of my experience when removed, so it's possible that the causes of those aspects reside outside my brain. That said, I don't find it likely; I'm inclined to agree that the causes of my experience reside in my brain. I still don't care much what label we attach to those causes, and I still think the label "qualia" causes more confusion due to conceptual baggage than it resolves.

Re #3: I see no reason at all to believe this. The causes of experience are no more "clearly a basic fact of physics" than the causes of gravity; all that makes them seem "clearly basic" to some people is the fact that we don't understand them in adequate detail yet.