Regarding Transubstantiation, there is absolutely zero reason to think that the disciples with whom Jesus shared his Last Supper thought that there was some sort of "ah hah!...now you're really drinking my blood!" magic trick going on. I don't think we have any reason to look at what Jesus did and didn't mean in any other way than that which was understood by the disciples.... And, I say that we mustn't think we are to believe it in a way different from what Jesus communicated to his followers there in that room.1. Transubstantiation is not a magic trick. (Don't misrepresent Catholic teaching.)
2. There is an ambiguity in the second sentence, for "that which was understood by the disciples" can be taken to mean either (a) the things understood by the disciples at that moment in the upper room, or (b) the things understood by them after the Resurrection. If used in the first sense, I strongly disagree; if used in the second, I strongly agree. (1) The apostles only began to really comprehend Christ's passion (at the earliest) a week or so after the Resurrection. Before then, neither the apostles nor the disciples on the road to Emmaus understood what had passed, for not only did the disciples run away but some, like Peter, even returned to their previous occupations. If we are to only understand Christ to mean what the apostles then understood him to mean, we must (in order to be consistent) reject the Atonement and Resurrection, since the disciples understand neither one. (2) The language of John 6 does not seem to be metaphorical. Many found it a hard teaching (and many still do). Yet if Christ did not mean it in some literal and profound way he could have qualified his statement and prevented the misunderstanding. Moreover, Christ's own words on the subject do not appear figurative. They were not in the context of a parable but in the course of a meal. "This is my body" is so strongly and simply put that to explain it as figurative seems dubious. Finally, Paul's rebuke to the Corinthians witnesses to the same faith. After repeating the very words of Christ, he says, "Whoever, therefore, eats the bread or drinks the cup of the Lord in an unworthy manner will be guilty of profaning the body and blood of the Lord." Only sacred things can be profaned, and "the body and blood of the Lord" is certainly sacred.
3. In a debate on Transubstantiation this third sentence is insufficient and begs the question. To say because we must believe only what Christ communicated to his apostles and therefore we should not believe the Catholic doctrine, assumes that what Christ communicated to his apostles was in fact what the Protestant side claims it is. But that is the very point in question; consequently, you have assumed your conclusion to be true in your "argument" for its truth.