IT IS ALL PROPHETIC (bare with me):

Oh, where have you been, my blue-eyed son
And where have you been, my darling young one

In Islam, the "white man" is described as the blue eyed deamon, which in this case, a "white man" can de described as a "Christian Man", it being known to Dylan and many Middle Eastern natives as a western faith in modern times. The Blue Eyed son could be Jesus upon his return or could also speak of profets, or even the antichrist. Reference "Sounds of Silence", which states: "The signs of the prophets are written on the subway walls.", also "Times are Changing" has Dylan stating "Come writers and critics, who are prophets with your pens..the chance won't come again (implying urgency in the matter). "Those whose time is worth saving (The Bible says that those who want to keep (Earthly) lives will lose them and that the last will be first. For the loser now will be later to win
For the times, they are a-changin'"
You can find Biblical reference in many Rock N Roll Songs.
The book of Apocalypse states that there will be Thunder, Voices, and an Earthquake when the time has come. "Have you ever seen the rain" -Could be accompanied by a Thunder and a "Hard Rain", while it is also said that the son of God will come as lightning and that even so people will still lack faith in the rapture, it is said the speed of light (like lightning) can surround the earth 7.5 times in a single second.
Ok getting carried away, lets continue.

I've stumbled on the side of twelve misty mountains
(?)

I've walked and I've crawled on six crooked highways
(?)

I've stepped in the middle of seven sad forests
(7 continents)

I've been out in front of a dozen dead oceans
(7 seas +5 Oceans)

I've been ten thousand miles in the mouth of a graveyard
10k in the Bible is a number that represents an endless count, which could be a metaphor for Jesus suffering damnation and Death for us, still ultimately defeating it.

And it's a hard, and it's a hard, it's a hard, and it's a hard
It's a hard rain's a-gonna fall
(End of times)

Oh, what did you see, my blue-eyed son
And what did you see, my darling young one

I saw a newborn baby with wild wolves all around it
(?)

I saw a highway of diamonds with nobody on it
Diamonds "live forever": which could mean the path to faith or righteousness. Unsure though.

I saw a black branch with blood that kept drippin'

I saw a room full of men with their hammers a-bleedin'
(Oil Drilling. It is said that those who drink the nectar of the Eufrates which is a river which is now in what used to be Babylon will be judged. My opinion is that the nectar is petrol.)

I saw a white ladder all covered with water
(Water is the only thing that isn't mentioned in creation, so there was always water for Gods spirit to cover, even in Eternity, it making sense to have a correlation to The End as much as the beginning :Higher up.)

I saw ten thousand talkers whose tongues were all broken
"Voices of the apocalypse."
And there were flashes of lightning, and voices, and thunders; and there was a great earthquake, such as there had not been since men were upon the earth--so great was the earthquake, so mighty,-States Revelation 16;18

I saw guns and sharp swords in the hands of young children
(War)-Could mean militia recruited children but unsure.

And it's a hard, and it's a hard, it's a hard, it's a hard
It's a hard rain's a-gonna fall

And what did you hear, my blue-eyed son?
And what did you hear, my darling young one?
I heard the sound of a thunder that roared out a warnin'

And there were flashes of lightning, and voices, and thunders; and there was a great earthquake, such as there had not been since men were upon the earth--so great was the earthquake, so mighty,-Revelation

Heard the roar of a wave that could drown the whole world
Heard one hundred drummers whose hands were a-blazin'

Usually speaking of drums pre-war. Still unsure.

Heard ten thousand whisperin' and nobody listenin'

Again the voices in revelation, madness, silent cries of the oppressed.

Heard one person starve, I heard many people laughin'

It is a spiritual ritual to stop eating but Christ states that the ritual he loves in this manner is to give to the poor, and love one another, otherwise it'd be useless to starve yourself.

Heard the song of a poet who died in the gutter
Heard the sound of a clown who cried in the alley

There are two prophets in the book of Revelation who will judge but ultimately be killed in suffering.

And it's a hard, and it's a hard, it's a hard, it's a hard
It's a hard rain's a-gonna fall
Oh, what did you meet, my blue-eyed son?
Who did you meet, my darling young one?

I met a young child beside a dead pony
(?) It is said the first horseman will carry a bow. Saggitarius? One of the brightest stars at the beginning of 2020 (40), was that which belonged to the sagitarius constellation, along with Draco and Serpens (The Dragon and The Small Snake).

I met a white man who walked a black dog
(?)

I met a young woman whose body was burning
It could mean lust, could mean the warning of pregnancies during end of times (also biblical).

I met a young girl, she gave me a rainbow
(¿Gender equality?)

I met one man who was wounded in love
I met another man who was wounded with hatred

Wounded in love (Jesus) and hatred (Satan)?

And it's a hard, it's a hard, it's a hard, it's a hard
It's a hard rain's a-gonna fall
And what'll you do now, my blue-eyed son?
And what'll you do now, my darling young one?

I'm a-goin' back out 'fore the rain starts a-fallin'
Before the end.

I'll walk to the depths of the deepest black forest
One of the seven sad Forrests (continents)

Where the people are many and their hands are all empty
Where do you think?

Where the pellets of poison are flooding their waters
???

Where the home in the valley meets the damp dirty prison
Almost..

And the executioner's face is always well hidden
Where hunger is ugly, where souls are forgotten
(No food, nor Christianity)

Where black is the color, where none is the number
(Race and Faith)-AFRICA.

And I'll tell it and think it and speak it and breathe it
Preaching from the Spirit.

And reflect it from the mountain so all souls can see it
Then I'll stand on the ocean until I start sinkin'
Until faith wavers.

But I'll know my song well before I start singin'
And it's a hard, it's a hard, it's a hard, it's a hard
It's a hard rain's a-gonna fall

It is all, already written.