Re: Moses and Elijah, both of their bodies were allegedly taken up to Heaven. (St. Jude talks about the Moses bit in his Epistle, if I recall correctly.)
Re: saintly apparitions and visions in general, we aren’t seeing the souls of saints. Either we are seeing an appearance created by God; or we are seeing a vision created by God in the imaging areas of our brains. Either way, it’s a convenient interface for our poor minds, but not the point of what’s going on. (And indeed, St. John of the Cross points out that in any kind of experience of this kind, the real point is the way God is helping our souls grow, which is done “behind our backs” so that we don’t even notice.)
Re: the magisterial definition of “soul,” Father Hardon had good info in his Modern Catholic Dictionary:
SOUL: The spiritual immortal part in human beings that animates their body. Though a substance in itself, the soul is naturally ordained toward a body; separated, it is an “incomplete” substance. The soul has no parts, it is therefore simple, but it is not without accidents. The faculties are its proper accidents. Every experience adds to its accidental form. It is individually created for each person by God and infused into the body at the time of human insemination. It is moreover created in respect to the body it will inform, so that the substance of bodily features and of mental characteristics insofar as they depend on organic functions is safeguarded. As a simple and spiritual substance, the soul cannot die. Yet it is not the total human nature, since a human person is composed of body animated by the soul.
“Form” in this case does not mean “shape.” It’s the philosophical and theological term. Here’s its definition.
FORM: The nature or essence of a thing; the internal specific principle of the distinctive nature or activities of any created being. Also, after a change, the new feature(s) in whatever has been changed. Contrasted with “matter” in scholastic philosophy and theology.
Because every soul is individually created by God and individually infused into its body by God, there is no possible mismatch between soul and body. Every single one of our souls is a custom design job!
This doctrine is also a rebuke to the pagan Greek philosophers and cults, who often taught stuff like that women had no immortal soul, that some people were natural slaves with weaker souls, or that women had to reincarnate into becoming men before their souls could become perfected.
Re: soul and body and the sex of the body, I am surprised that nobody has pointed the poster toward St. John Paul II’s papers on the Theology of the Body.