Regarding your question on when they realised fully that Jesus would be present in the Eucharist, it seems to me that this would have been completely clarified at the Last Supper. As you pointed out, some time before the Last Supper, Christ told His apostles that He is the Bread of Life and then that unless they eat the flesh of the Son of Man and drink His blood, they would have no life in them. From then they believed that they would have to do this, but it was not until the Last Supper that they were told how - that they would eat His body and drink His blood under the appearence of bread and wine. I’m willing to be corrected of course, but I would say that John 6 was the first step in the revelation of the Eucharist to the Apostles.
Your Fundamentalist friend is making a standard argument against the Eucharist - that there was no transubstantiation. The term transubstantiation began to be used to consisely define the nature of the Eucharist in the thirteenth century, however that does not mean that transubstantiation did not actuall occur just because that wasn’t the term originally applied to it. Scripture is very clear that we must actually eat the flesh of Christ rather than symbols. It is interesting that the only time we hear of disciples leaving Christ for doctrinal reasons is when He tells them “I am the living bread which has come down from heaven; he who eats this bread will live forever; and the bread that I will give for the life of the world is my flesh…unless you eat the flesh of the Son of Man and drink His blood you have no life in you…” Jesus knew people were offended by this - to those who didn’t believe, He was suggesting cannibalism and drinking blood which Jewish law forbade. If the Lord were merely speaking symbolically why did He not explain this to the disciples who had turned their backs on Him? Peter, on the other hand, speaking for the Twelve trusted in Jesus and accepted what He told them - “Lord, to whom shall we go? You have the words of eternal life…” This to me is actually the most compelling argument for the true presence in the Eucharist - if Jesus were merely speaking metaphorically the disciples would have known. How many times are we told in Scripture that Jesus told them a parable? Many indeed, because either Christ told them or it was clear to them - with the Eucharist, strange as it is, the disciples know that Christ is speaking the truth clearly. The same applies to the Last Supper - “This is my body… This is my blood…” - there is no symbolism here, it is as Jesus is telling them. The apostles knew this, the Early Church Fathers knew this, and it was many centuries before the idea of the True Presence was seriously challenged… Some passages from the Early Church Fathers would be useful in understanding what the Early Church thought of the Eucharist, though non-Biblical sources may not interest your friend. Finally, it may be useful to ask your friend why Paul tells us that those who receive the Eucharist unworthily shall be guilty of the body and blood of Christ. If the Eucharist is only a symbol - bread and wine - how can that make us guilty of the body and blood of Christ?
With regard to your first question, I cannot answer it off-hand, but they certainly knew before Pentecost. Even in the passage we spoke of earlier - John 6 - Peter assures Christ that they know that He has the words of eternal life and that they had already come to know that He was the Holy One of God.