He is speaking literally in John 4, for Baptism is literally in water. Same as in John 6, where the Eucharist is literally His flesh and blood and the soul.
the object of faith is in Christ alone, not in the Eucharist
Correct, but it seems to me you say "Christ alone" to you means something like "Christ apart from that Catholic stuff He teaches by mistake". "Observe all things whatsoever I have commanded you" (Matthew 28:20) means also to observe this:
Amen, amen I say unto you: Except you eat the flesh of the Son of man, and drink his blood, you shall not have life in you. He that eateth my flesh, and drinketh my blood, hath everlasting life: and I will raise him up in the last day. (John 6)
the source of the condemnation is not in the elements themselves, or in the water of baptism, but in the faithlessness and the sin of the individual who is unworthily receiving.
The condemnation results from sin, yes; and it is Jesus Who condemns, yes again. But the sin in focus is believing that Protestant stuff that denies the Eucharist, rather than what Christ says and the Holy Scripture records. Paul specifically explains what the sin is: "not discerning the body of the Lord" (1 Cor. 11:29).
WRONG. Jesus does NOT condemn.
John 3:17