Ecclesiastes 11:5 reflects an ancient conundrum of the ancient Jewish world. Because the forming of Adam was unique in that he was sculpted from clay and directly animated by God breathing into the clay with breathe from his own lungs and yet babies are born without such animating breathing. So how do babies become animated? How is the breath of life passed from the mother to the little ones?:
[Ecclesiastes 11:5 YLT] (5) As thou knowest not what [is] the way of the spirit [IE: the breath of life], How -- bones in the womb of the full one, So thou knowest not the work of God who maketh the whole.
I don't really think that is the main verse he has in mind, though. I mean, it is a related idea but I think John 3 is more about the hidden inner leading of a person born from above, as seen here:
[Isaiah 40:13-14 NASB20] (13) Who has directed the Spirit [IE: wind] of the LORD, Or as His counselor has informed Him? (14) With whom did He consult and [who] gave Him understanding? And [who] taught Him in the path of justice and taught Him knowledge, And informed Him of the way of understanding?
The footnote regarding "directed" reads:
(40:13) Or measured, marked off
In other words, who can trace the path of the wind? Or predict or direct it?
Proverbs says that trying to control a contentious woman is as futile trying to constrain the wind with oil on his hands!:
[Proverbs 27:15-16 NASB20] (15) A constant dripping on a day of steady rain And a contentious woman are alike; (16) He who would restrain her restrains the wind, And grasps oil with his right hand.
There is a mysterious, invisible and uncontrollable path that the wind takes. So too, those born from above are winds, led by the inner wind of God.
[Psalm 104:4 NASB20] (4) He makes the winds His messengers, Flaming fire His ministers.
Paul quotes the same passage from the form in the Greek translation:
[1 Corinthians 2:14-15 NASB20] (14) But a natural person does not accept the things of the Spirit of God, for they are foolishness to him; and he cannot understand them, because they are spiritually discerned. (15) But the one who is spiritual discerns all things, yet he himself is discerned by no one.
Interestingly, Hebrews quote the Greek of Psalm 104, but gets it backwards, but it works better with John 3:8!:
[Hebrews 1:7 NASB20] (7) And regarding the angels He says, "HE MAKES HIS ANGELS WINDS, AND HIS MINISTERS A FLAME OF FIRE."
Paul reads the Greek scriptures in a way that is compatible with the sense of John 3:8 and the Hebrew of Isaiah 40:13, even though it has been corrupted in the transmission.
So long story short, I think the Isaiah 40 passage, from the Hebrew, not the Greek, is more what John 3:8 has in mind, while Paul is commenting on the Greek of that same passage. The Ecclesiastes passage is more concerned with the mystery of the transmission of the breath of life from Adam, to Eve and then to the babies.
By the way, Ecclesiastes also ponders the mystery of what happens to the breath of life when a person, human or animal, dies:
[Ecclesiastes 3:19-21 NASB20] (19) For the fate of the sons of mankind and the fate of animals is the same. As one dies, so dies the other; indeed, they all have the same breath, and there is no advantage for mankind over animals, for all is futility. (20) All go to the same place. All came from the dust and all return to the dust. (21) Who knows that the spirit of the sons of mankind ascends upward and the spirit of the animal descends downward to the earth?