1) As far as I understand it, atoms don't have a specific 'location', there are only probabilities for where that atom might be at any given time. Given that it is silly to speak of individual atoms. Even if I misunderstood that part, it is still the case that two entities which have no discernible difference in principle are the same, as a matter of simple logic.

2) Asking "which body do you wake up in" is a wrong question. It is meaningless because there is no testable difference depending on your answer, it is not falsifiable even in principle. The simple fact is that if you copy Sophronius, you then have 2 Sophronius waking up later, each experiencing the sensation of being the original. Asking whose sensation is "real" is meaningless.

3) It is not a non-sequitur. Sleep interrupts your continuity of self. Therefore, if your existence depends on uninterrupted continuity of self, sleep would mean you die every night.

I notice that you keep using concepts like "you", "I" and "self" in your defence of a unique identity. I suggest you try removing those concepts or any other that presupposes unique identity. If you cannot do that then you are simply begging the question.