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As you mentioned in your question, Jung was less than perfectly consistent in his definition of archetype throughout his career. This ambiguity reflects the continuing debate about semantic representation in the brain.

His early work stressed the emergence of archetypes as fundamental dichotomies of self experience- whose Enantiodromaic character was the origin of their emergence in the psyche. Thoughts are either expressed or not expressed, whence the self is divided into Persona and Anima; thoughts (at least if one takes Jung at his word in his characterisation of thought as Libido) provide desire or fear, whence Ego and Shadow. This presents a potential picture of Jungian archetypes in the brain as primarily distributed phenomena-a set of pairwise partitions of the conscious brain.

His later writings, however, while still shewing their enantiodromia in their dialectical function, are more liberal concerning their origin. Concerning the Senex archetype for example; is a thought either that of a young or old man? -I would doubt it. The archetypes of these later writings are much more amenable to so-called 'sparse' representation.

Sparse representation is the (to borrow a term!) enatiodromaic opposite of distributed, in which small populations of neurons, or even single neurons can code for a given semantic character. Under assumptions of sparse representation, hypothetical 'Grandmother cells' could code for whole semantic classes, and so archetypes themselves.

Evidence for sparse representation has been found implicating the Medial Temporal Lobe in representing semantic classes across sensory modalities in single neurons (Quiroga et al., 2005). This is however hotly contested, and experimental limitations abound (there's a nice microcosm of the debate at the wiki page for Grandmother Cell, which also features a potted summary of the linked experiment).

References

Quiroga RQ, Reddy L, Kreiman G, Koch C, Fried I. (2005) Invariant visual representation by single neurons in the human brain. Nature 435, 1102-1107. http://www.nature.com/nature/journal/v435/n7045/full/nature03687.html