I'm not an expert on the JFK assassination or Freemasonry but here is my maybe-serious attempt at Dylanology.
If there are two quote blocks the first is lyrics from Murder Most Foul and the second is from King-Kill 33: Masonic Symbolism in the Assassination of John F. Kennedy
by James Shelby Downard. There are some parallels between the two. If there is a single quote block it is from Murder Most Foul unless otherwise stated.
The day they blew out the brains of the king
Downard's thesis is that the Kennedy assassination was a Masonic "Killing of the King" ritual. There is of course that "Camelot" thing but that is the exoteric reading. I am giving the esoteric reading. The title refers to Hamlet, a play about the murder of a king, but I think a lot of Shakespeare plays are about murdered kings. Downard specifically mentions Macbeth as being symbolically important and Dylan throws in a line about Lady Macbeth later in the song.
Being led to the slaughter like a sacrificial lamb
Killed him like a human sacrifice
Downard says that the Kennedy assassination was a human sacrifice for some greater Masonic end, the moon landing perhaps: "for the placing of the Freemasons on the moon could occur only after the Killing of the King." I don't think Neil Armstrong was a Freemason.
We've already got someone here to take your place
Lyndon Johnson would have replaced Kennedy no matter how he died but Downard identifies him as a Freemason. Wikipedia says:
In addition to the individuals listed above, Lyndon B. Johnson was initiated into the first degree of Freemasonry – "Entered Apprentice", October 30, 1937 in Johnson City Lodge No. 561, at Johnson City, Texas, but did not advance any further and did not become a full member of his lodge.
So he was probably a top secret undercover Mason who had most of his Masonic background sheep-dipped.
Perfectly executed, skillfully done
Hiram Abiff is by legend the Freemason who built Solomon's Temple. A description of him and his work in 2 Chronicles 2:13-14 makes frequent use of the word "skillful":
13 And now I have sent a skillful man, endowed with understanding, Huram my master craftsman 14 (the son of a woman of the daughters of Dan, and his father was a man of Tyre), skilled to work in gold and silver, bronze and iron, stone and wood, purple and blue, fine linen and crimson, and to make any engraving and to accomplish any plan which may be given to him, with your skillful men and with the skillful men of my lord David your father.
Maybe that is a stretch but Masons tell a story that Hiram Abiff was killed in the original Killing of the King ritual, even if they do not call it that.
Slide down the banister, go get your coat
It’s unfortunate that President Kennedy didn’t trip Tito and then slide down the stair-rail, for he was in a very vulnerable position as related to Masonic sorcery, and such unorthodox action might have rattled the "Prince of Harodim."
Both men reference sliding down banisters. A little odd but could be a coincidence. Could also be an oblique reference to Guy Banister.
Stack up the bricks, pour the cement
That is a literal description of masonry.
Put your foot in the tank and then step on the gas
Try to make it to the triple underpass
Blackface singer, whiteface clown
Better not show your faces after the sun goes down
The limo drove through the triple underpass from Dealey Plaza. Triples are significant to Downard. He also refers to Kennedy as the Sun God. So Dylan could be saying that the assassins need to drop out of sight after they kill Kennedy. Downard:
As for the three assassins themselves:
Perry Raymond Russo told a New Orleans grand jury that [CIA agent David] Ferrie said [regarding the assassination of JFK] that "there would have to be a minimum of three people involved. Two of the persons would shoot diversionary shots and the third ... shot the good shot." Ferrie said that one of the three would have to be the "scapegoat." He also said that Ferrie discoursed on the availability of exit, saying that the sacrificed man would give the other two time to escape. (Quoted by W.H. Bowart in Operation Mind Control).
I guess the two assassins are the blackface singer and whiteface clown and Oswald would be the scapegoat. Al Jolson died in 1950 so Dylan can't be fingering him.
As for David Ferrie:
Ferry 'cross the Mersey and go for the throat
One reading of that line could be, "[David] Ferrie, have no mercy and shoot him through the throat." A bullet exited Kennedy's throat. David Ferrie is featured in other theories. This line actually follows the banister line which is perhaps interesting because Guy Banister and David Ferrie were acquaintances.
Downard compares the three tramps to the three men who murdered Hiram Abiff. Their only real significance in his theory is that there were three of them. Dylan mentions the tramps in a line but like David Ferrie other conspiracy theories make use of them too.
What is the truth, and where did it go?
Ask Oswald and Ruby, they oughta know
"Shut your mouth," said a wise old owl
The owl is an Illuminati symbol
for knowledge or something like that and the Illuminati had strong links with Freemasonry. I guess you could read this as the cover-up.
Where we ask no quarter, and no quarter do we give
We're right down the street, from the street where you live
The Supreme Council, 33°, Scottish Rite Freemasonry, Southern Jurisdiction is down the street from the White House. I didn't know this beforehand but figured something like it would be true based on the song's undeniable references to Freemasonry.
Wake up, little Susie, let's go for a drive
Cross the Trinity River, let's keep hope alive
James Shelby Downard goes on and on about the significance of threes specifically mentioning the Trinity River, the triple underpass, and lots of other things. Not very strong but I'm keeping it in.
Zapruder's film I seen night before
Seen it thirty-three times, maybe more
He could have said twenty-two or forty-four but went with thirty-three. Twenty-two would be more alliterative. Maybe he really has seen it thirty-three times. Or maybe he is referencing the thirty-third degree of Freemasonry. Downard is obsessed with the 33rd degree and the number 33.
They killed him on the altar of the rising sun
Fredericksburg is also the location of the "House of the Rising Sun," a masonic meeting place for such notables as founding fathers George Washington and Benjamin Franklin (of Hell-Fire Club fame) and George Mason.
Of course he wasn't killed in Fredericksburg but the assassination was the culmination of a ritual that began with the Freemasons who founded this country.
They mutilated his body and they took out his brain
What more could they do? They piled on the pain
But his soul was not there where it was supposed to be at
For the last fifty years they've been searchin' for that
They killed him once and they killed him twice
The concealment of the body was called "aphanism" and is a rite of the Masonic 3rd Degree...
If and when the brain is recovered, the entire process will have been completed under the term "euresis."
Maybe a stretch, but in the Freemason ceremonial ritual resurrection occurs after the discovery of the body but Kennedy's brain has been "lost", preventing his resurrection thus killing him for a second time.
I hate to tell you, mister, but only dead men are free
This line may also have to do with the ceremonial death and resurrection that is part of Masonic initiation ritual.
Play it for the man with the telepathic mind
Oswald may have undergone biotelemetry implantation in the Soviet Union while a "volunteer" at a Behavior Control Center at Minsk.
That would not technically be telepathy but nobody has heard of a telemetric mind. The next lines are:
Play John Lee Hooker, play "Scratch My Back"
Play it for that strip club owner named Jack
Guitar Slim going down slow
Play it for me and for Marilyn Monroe
Oswald being placed with Jack Ruby and Marilyn Monroe seems right.