My best bet is that the self is a single physical thing, a specific physical phenomenon, which forms at a definite moment in the life of the organism, persists through time even during unconsciousness, and ceases to exist when its biological matrix becomes inhospitable.

This is just another way of saying you believe in a soul. And if you think it persists during unconsciousness then why can't it persist during freezing?

For example, it might be an intricate topological vortex that forms in a (completely hypothetical) condensate of phonons and/or biophotons, somewhere in the cortex.

This sentence is meaningless as far as I know.

But what is really unlikely is that I am just a virtual machine, in the sense of computer science - a state machine whose states are coarse-grainings of the actual microphysical states, and which can survive to run on another, physically distinct computer, so long as it reproduces the rough causal structure of the original.

You say it's unlikely but give no justification. In my opinion it is a far more likely hypothesis than the existence of a soul.

I am surprised that a comment like this has recieved upvotes.