The Jew’s understood him as literally meaning the stone Temple on Mount Zion. Jesus literally meant the true Temple of His body, the place where God’s earthly presence dwells. I don’t think you’re going the word metaphor correctly in this case. Anyway, I see your point as further supporting the real presence. Jesus spoke in a way regarding the Temple that wasn’t clarified then and wasn’t understood until after the Resurrection. Likewise, Jesus offered no correction or explanation to his Apostles by what he meant in regards to eating His flesh. This also wasn’t understood until after the Resurrection.
First, let me be clear that I don’t believe transubstantiation was invented at any time. That the Church has from its conception taught the real presence and the real reception of Jesus in the Eucharist, that it is truly His body and blood, and that it is a partaking of the divine nature, is a tenet of apostolic faith, Catholic and Orthodox.
My point is that John 6 was not something new or prior to tradition, nor is it independent of it. It always has in mind Christian teachings and traditions that predated it, and gives theological meaning to these traditions. It was and is a catechesis on the real presence in communion, especially in the first century. That is, it’s not a retroactive reading on our part, but John specifically and intentionally recording these words of Jesus here as a first century explanation of the real presence. John is not just thinking of those who left Jesus by the Sea of Galilee, he is also thinking of and speaking to those in the early Church community around 90 AD who found the real presence to be a “hard teaching.” There is a reason John wrote this, tied it into the manna of the Israelites, and did not write another summary of the words of institution.
And I don’t think John is a fool. I’m only saying that holding that the bread of life discourse is not a defense of the real presence seems to lead to the conclusion that John’s a fool. John was not writing prior to the Christian community, he was writing during it and after it had already become established, after the Communion meal was an established part of Christian worship. When John writes:* "53 Jesus said to them, “Very truly I tell you, unless you eat the flesh of the Son of Man and drink his blood, you have no life in you. 54 Whoever eats my flesh and drinks my blood has eternal life, and I will raise them up at the last day. 55 For my flesh is real food and my blood is real drink. 56 Whoever eats my flesh and drinks my blood remains in me, and I in them. 57 Just as the living Father sent me and I live because of the Father, so the one who feeds on me will live because of me. 58 This is the bread that came down from heaven. Your ancestors ate manna and died, but whoever feeds on this bread will live forever.” 59 He said this while teaching in the synagogue in Capernaum.*, he is thinking of the Eucharist and is teaching on the Eucharist. If he’s not writing on the real presence, and if he is fully knowledgeable that Christians eat the communion meal calling it the flesh and blood of Christ (as a non-literal metaphor, if we deny the real presence), then he’d have to be very, very foolish to think this wouldn’t cause scandal and heresy in stressing multiple times that Jesus’ flesh must be eaten and gnawed and that it is true food and *true *drink (and not metaphorical food and drink), especially since he gives no clarification or correction. It’s not just John’s words taken alone, but John’s words in the context of first century Christian worship. It really doesn’t make sense if the real presence was not what he intended and an already accepted belief.