You would not need the simulation to be perfect; there is ample evidence that our brains a quite robust against disturbances.
> just because you simulated a brain atom by atom, does not mean you have a consciousness.
If you don't want that to be true, you need some kind of magic, that makes the simulation behave differently from reality.
How would a simulation of your brain react to an question that you would answer "consciously"? If it gives the same responds to the same inputs, how could you argue it isnt't conscious?
> If it is the arrangement of matter that gives rise to consciousness, then would that new consciousness be the same person or not?
The simulated consciousness would be a different one from the original; both could exist at the same time and would be expected to diverge. But their reactions/internal state/thoughts could be matched at least for an instant, and be very similar for potentially much longer.
I think this is just Occams razor applied to our minds: There is no evidence whatsoever that our thinking is linked to anything outside of our brains, or outside the realm of physics.
