First, verse 63 gives the answer to what Jesus was referring to.
Not even a little bit.
From a paper I wrote some time back:
Grasping at Straws: John 6:63
“The Spirit gives life; the flesh counts for nothing. The words I have spoken are spirit and they are life.” (John 6:63)
These words were spoken by Jesus shortly after delivering his teaching on the Eucharist, and some people claim that they indicate that Jesus was speaking figuratively when he commanded us to eat his body and drink his blood. However, this would be a misunderstanding of what Jesus meant when he said, “the flesh counts for nothing.”
First, notice that whenever Jesus referred to his own body and blood, he said “my flesh” or “the flesh of the Son of Man”. Here are the examples:
“This bread is
my flesh, which I will give for the life of the world.” (John 6:51)
"Jesus said to them, “I tell you the truth, unless you eat
the flesh of the Son of Man and drink his blood, you have no life in you. Whoever eats
my flesh and drinks
my blood has eternal life, and I will raise him up at the last day. For
my flesh is real food and
my blood is real drink. Whoever eats
my flesh and drinks
my blood remains in me, and I in him.” (John 6:53-56)
At this point, the narrative explains that the disciples were on the verge of revolt over this teaching. Jesus tells them that they cannot understand this teaching with their natural minds. Here is the verse in context: “On hearing it, many of his disciples said, ‘This is a hard teaching. Who can accept it?’ Aware that his disciples were grumbling about this, Jesus said to them, ‘Does this offend you? What if you see the Son of Man ascend to where he was before! The Spirit gives life; the flesh counts for nothing. The words I have spoken to you are spirit and they are life.’” (John 6:60-63)
In John 6:63, Jesus uses the phrase “the flesh” instead of “my flesh” or “the flesh of the Son of Man” because he is not talking about his own body; he is referring to man’s natural, unenlightened rational intellect.
Jesus tells the grumbling Jews (who can’t understand
how he would give them his flesh to eat) that they cannot grasp it with their natural minds because it is a mystery beyond the ability of “the flesh” to understand. This is the same manner of speaking used by Paul in 1 Corinthians 2 & 3 when he is distinguishing between fleshly or carnal Christians and those who are discern the things of God with their spirits.
Second, it might be worth noting the obvious fact that Jesus cannot be saying that HIS own flesh “counts for nothing”; otherwise, his death upon the cross would be meaningless. Instead, we know that his own body, his flesh, was broken and pierced for our sake; no Christian would deny that. Therefore, since HIS flesh does count for something, he must have been referring to “flesh” other than his own in v. 63.
Thus, the one verse that many Protestants cling to as an argument against the Real Presence of Christ in the Eucharist does not mean what they falsely claim it means. Ironically, their “proof text” points out precisely why they cannot understand the Eucharist: they are using their flesh instead of their spirits to discern the things of God. Unfortunately, their flesh “counts for nothing”.