Thank you to my two colleagues who have reminded me that I am but a probie in the philosophical guild, and as such still don't understand everything perfectly. I moved too quickly in my explanation and made a mistake at the end.
I said that transubstantiation was an example of substantial change. This is not quite correct.
Matter is what individuates particular things: while my dog and your dog may both have the form of "dog," they are not the same dog because those two forms do not stand in (i.e. are not instantiated in) the same primary matter. The form and the matter together make up the substance. In any substantial change, the form (that is, that which makes the thing to be what it is) of the new substance is educed from the matter (that is, possibility of being) of the old substance. This is what allows us to say that there is some sort of continuity of being when things change, that things don't just pop into existence out of nowhere. In my attempts to explain act-potency, form-matter, and substance-accident, my examples involved just such instances of a new substance coming into being.
But because in the mystery of transubstantiation we have, not a new substance coming into being, but rather one substance becoming another, already existing substance or exisiting thing, the change does not occur in the same way, and thus cannot properly be called "substantial change." In the Mass, the bread and wine become the Body and Blood of Christ; they become Jesus. It's not that Jesus springs into being where He didn't exist before; but rather Jesus, already existing, now becomes present such that where the bread and wine once existed, He now exists--you can point to the species (appearances) and say, "That's Jesus."
The whole substance of the bread and wine becomes the whole substance of Christ: body, blood, soul, and divinity. And as we defined "substance" as "form plus matter," in order for the substance of the bread and wine to become the substance of Christ, that which was bread and wine must take on not only the form of Christ, but also the matter of Christ.
At best, we could say that transubstantiation is a very special and unique sort of substantial change that works very differently from any other instance.
Again, I reiterate that these philosophical explanations can be helpful in pointing us toward what happens in the mysteries of the faith, but they can never come close to exhausting them or wholly explaining them. Which is why it's so easy to get them wrong. :)