Sam Harris is being completely consistent here. You are running together two separate claims:

Claim 1: Consciousness cannot be reduced to physical brain-states/processes because we have to take into account the phenomenal, qualitative, experiential side.

Claim 2: There is a self.

These two claims are logically independent of one another. That is, prima facie, one can completely coherently deny one and affirm the other, affirm both, or deny both. To my understanding, in what you label (S1) and (S2), Harris endorses Claim 1. In the later part of the video that you identify, he switches topics and denies Claim 2. Harris says that the self is an illusion, but notice that he is thinking of the self in phenomenal terms; to say there is no self is to say that there is no "substance" that acts as the "locus" of conscious experience; that all conscious experiences are bundled together without the "glue" of a central self. But notice that does not deny conscious experience -- it affirms it! Moreover, one could be a strict physicalist, arguing that all conscious experience can be reduced out of the theory in favor of physical primitives. Yet, such a theorist could still hold that there is a self!

Sartre is a good example, say, of someone who is absolutely not a physicalist about consciousness and yet argues that there is no Ego, no self, underlying and gluing together all of one's experiences.

In short: In your assessment of Harris' article, you seem to identify consciousness with the self. But these are two separate things. One's view on the status of physicalism about consciousness and one's view on the ontological status of the self are two completely different matters.

Sam Harris is being completely consistent here. You are running together two separate claims:

Claim 1: Consciousness cannot be reduced to physical brain-states/processes because we have to take into account the phenomenal, qualitative, experiential side.

Claim 2: There is a self.

These two claims are logically independent of one another. That is, prima facie, one can completely coherently deny one and affirm the other, affirm both, or deny both. To my understanding, in what you label (S1) and (S2), Harris endorses Claim 1. In the later part of the video that you identify, he switches topics and denies Claim 2. Harris says that the self is an illusion, but notice that he is thinking of the self in phenomenal terms; to say there is no self is to say that there is no "substance" that acts as the "locus" of conscious experience; that all conscious experiences are bundled together without the "glue" of a central self. But notice that does not deny conscious experience -- it affirms it! Moreover, one could be a strict physicalist, arguing that all conscious experience can be reduced out of the theory in favor of physical primitives. Yet, such a theorist could still hold that there is a self!

Sartre is a good example, say, of someone who is absolutely not a physicalist about consciousness and yet argues that there is no Ego, no self, underlying and gluing together all of one's experiences.

In short: In your assessment of Harris' argument, you seem to identify consciousness with the self. But these are two separate things. One's view on the status of physicalism about consciousness and one's view on the ontological status of the self are two completely different matters.