Searle's view is:

1. qualia exists (because: we experience it)
2. the brain causes qualia (because: if you cut off any other part of someone they still seem to have qualia)
3. if you simulate a brain with a Turing machine, it won't have qualia (because: qualia is clearly a basic fact of physics and there's no way just using physics to tell whether something is a Turing-machine-simulating-a-brain or not)

Which part does LW disagree with and why?

The whole thing: it's the Chinese Room all over again, a intuition pump that begs the very question it's purportedly answering. (Beginning an argument for the existence of qualia with a bare assertion that they exist is a little more obvious than the way that the word "understanding" is fudged in the Chinese Room argument, but basically it's the same.)

I suppose you could say that there's a grudging partial agreement with your point number two: that "the brain causes qualia". The rest of what you listed, however, is drivel, as is easy to see if you substitute some other term besides "qualia", e.g.:

1. Free will exists (because: we experience it)
2. The brain causes free will (because if you cut off any part, etc.)
3. If you simulate a brain with a Turing machine, it won't have free will because clearly it's a basic fact of physics and there's no way to tell just using physics whether something is a machine simulating a brain or not.

It doesn't matter what term you plug into this in place of "qualia" or "free will", it could be "love" or "charity" or "interest in death metal", and it's still not saying anything more profound than, "I don't think machines are as good as real people, so there!"

Or more precisely: "When I think of people with X it makes me feel something special that I don't feel when I think of machines with X, therefore there must be some special quality that separates people from machines, making machine X 'just a simulation'." This is the root of all these Searle-ian arguments, and they are trivially dissolved by understanding that the special feeling people get when they think of X is also a property of how brains work.

Specifically, the thing that drives these arguments is our inbuilt machinery that classifies things as mind-having or not-mind-having, for purposes of prediction-making. But the feeling that we get that a thing is mind-having or not-mind-having is based on what was useful evolutionarily, not on what the actual truth is. Searlian (Surly?) arguments are thus in exactly the same camp as any other faith-based argument: elevating one's feelings to Truth, irrespective of the evidence against them.