To clarify: the body becomes an animal-intelligence creature, and the spirit is an intelligent creature that takes only mental actions?

You say that they have different ability scores, saves, etc, but how does this work? Are they the same class, but with saves, BAB, etc calculated differently depending on different scores? Or do the two halves advance as separate characters - so, with the body as one class, and the spirit as another?

If they're, for example, one class, a psychic warrior - could the spirit manifest a power while the body attacks? If a warblade, could the body attack while the spirit manifests Iron Heart Surge?