I have found some time this morning to start on the link you provided. The Stanford Encyclopedia one.
You don’t seem to get it. It doesn’t matter one whit what the Stanford Encyclopedia says about " substance, " nor how ideologues interpret this in an attempt to smear the teachings of the Church. The O.P. will never agree with you, he is determined not to.
All that is improtant is to hold firmly to what the Church teaches. Remember that the Holy Spirit has guaranteed the Church can not err in matters of Faith and Morals. The Church is guided by Tradition, of which the Scriptures is a part, but only a part. And the final authority of this Tradition is the Magisterium of the Church.
In the doctrine of Christ’s Real Presence the Church has used the terms " substantially, " " substance, " " species, " and " transubstantiation. " It seems clear that the Church is borrowing these terms from philosophy, perhaps the philosophy of St. Thomas. But it is even more clear that it is using these terms in its own way to express the reality of Chris’s Presence and how we are to regard it and how we are to understand how this comes about.
And what this means is given in the Catechisl of the Catholic Church as follows :
1374 The mode of Christ’s presence under the Eucharistic species is unique. It raises the Eucharist above all the sacraments as "the perfection of the spiritual life and the end to which all the sacraments tend."199 In the most blessed sacrament of the Eucharist "the body and blood, together with the soul and divinity, of our Lord Jesus Christ and, therefore, the whole Christ is truly, really, and substantially contained."200 "This presence is called ‘real’ - by which is not intended to exclude the other types of presence as if they could not be ‘real’ too, but because it is presence in the fullest sense: that is to say, it is a substantial presence by which Christ, God and man, makes himself wholly and entirely present."201
1375 It is by the conversion of the bread and wine into Christ’s body and blood that Christ becomes present in this sacrament. the Church Fathers strongly affirmed the faith of the Church in the efficacy of the Word of Christ and of the action of the Holy Spirit to bring about this conversion. Thus St. John Chrysostom declares:
It is not man that causes the things offered to become the Body and Blood of Christ, but he who was crucified for us, Christ himself. the priest, in the role of Christ, pronounces these words, but their power and grace are God’s. This is my body, he says. This word transforms the things offered.202
and St. Ambrose says about this conversion:
Be convinced that this is not what nature has formed, but what the blessing has consecrated. the power of the blessing prevails over that of nature, because by the blessing nature itself is changed… Could not Christ’s word, which can make from nothing what did not exist, change existing things into what they were not before? It is no less a feat to give things their original nature than to change their nature.203
1376 The Council of Trent summarizes the Catholic faith by declaring: "Because Christ our Redeemer said that it was truly his body that he was offering under the species of bread, it has always been the conviction of the Church of God, and this holy Council now declares again, that by the consecration of the bread and wine there takes place a change of the whole substance of the bread into the substance of the body of Christ our Lord and of the whole substance of the wine into the substance of his blood. This change the holy Catholic Church has fittingly and properly called transubstantiation."204
1377 The Eucharistic presence of Christ begins at the moment of the consecration and endures as long as the Eucharistic species subsist. Christ is present whole and entire in each of the species and whole and entire in each of their parts, in such a way that the breaking of the bread does not divide Christ.205
There really is no point in going any futher than that. You do not have to Prove anything to Muze, he will not accept anything you say. So let it go. Besides, you are making mistakes here and there - which I really don’t feel inclined to unpack at this point. I will only say that St. Thomas would agree that the word :" substance " is validly applied to the " Whole Christ " just as it would to the " whole Socrates. " And it is clear that the act of " Transubstantiation " is very similar to what St. Thomas would call a substantial change - but of a very special kind. First we are talking about bread and wine being totally changed into the Entire Physical Human Nature of Christ and the Divine Nature of the Second Person of the Trinity. That makes this substantial change very different and unique - outside the normal definitions of philosophy.
And secondly, the species ( material accidents ) of the bread and wine remain, but they remain without a subject or substance in which to inhere. And this too makes for a substantial change that does not fit into the definition of a substantial change in St. Thomas.
And it is always these " accidents " with which science deals, but science would call them substances. And under normal circumstances, say before the consecration, we would agree. But after the consecration we know through Faith that bread and wine are no longer there but only their accidents ( philosophical accidents). Science would still disagree. Well, let it. Science does not recognize miracles.
And this is about all we can say.
LInus2nd