Identity is not merely emergent, because it is not coherent enough to constitute a tower of realizations. Although it is multiply realized, it is not just realized at different levels of complexity. It is realized multiply at every level of complexity, and higher level realizations do not supervene upon others.
I am a legal entity, a mind, a body, a collection of particles, etc. But I am multiple legal entities -- one for every legal contract into which I have entered. I can jointly and severally be parts of various groups and there is not some substrate on which those memberships are determined other than their own simple statement. I am multiple minds and bodies, past and future. And I am ambiguously a trail of particles across time, but which ones are really me is always ambiguous -- do I have a shirt, or is the shirt part of me when I wear it?
You might want to look at this 'monadically' in the sense of Leibniz or early Whitehead. The monad exists as the collection of all its effects on everything else. This allows each particle to be a monad, and for larger collections of things that have traceable effects in composite to also be monads. Identity applies at many levels and in many layers.
Whitehead argues that the imposition of static identity based upon physical composition is part of our mechanization of our sense of identity. You are focused upon the material identity. He argues for the primacy of the notion of an organism. When that organism has intelligence, his notion of organism comes very close to the modern psychoanalytic notion of intersubjectivity.
In a more organic view, things really cohere through procedural identity. An entity does not persist, but reiterates its roles in various circumstances. It is more important that my car is the thing that is available for me to drive, and for which I take a given set of responsibilities, and otherwise rely upon in various ways, than it is that it is made up of a given set of atoms, even in sequence over time. (Ask Phish.)
Identity obtains when one enters into relations with other things that have identities. Each thing is identical to itself in the sense that it has its own set of relationships and no other, and in basically no other way. We are made up of different particles, we occupy different spaces, we change both phsyically and psychologically across time, etc., etc. etc.
Identity establishes my assignment to various categories in different natural kinds, which, as Quine points out, are themselves incompletely separable. So identity, like existence is not really a property, much less one that can be clarified to the point of representing an emergent phenomenon.