I'm having difficulty understanding this. I tried to translate it into simpler English but there are parts of the text that I find hard to interpret.

Green hocker croakin'
In the Pygmy Twylyte

Crankin' an' a-coke'n
In the Winchell's do-nut Midnite

Out of his deep on a `fore day run
Hurtin' for sleep in the Quaalude Moonlight

Green hocker in a Greyhound locker
Smokin' in the Pygmy Twylyte

Joined the bus on the 33rd seat
By the doo-doo room with the reek replete

My version

Noob looser (jerk) smoking

In the Pygmy Twylyte (a reference to a drug maybe?)

Out of his mind drinking a coke (??)
In the Winchell's do-nut (at) Midnite

Out of his deep (out of his inner self ????) from selling drugs (on) the previous day
In need of sleep in the Quaalude Moonlight (again a reference to drug)

Noob looser in a Greyhound locker (is 'locker' here a reference to a small bus)
Smokin' in the Pygmy Twilight

Joined the bus on the 33rd seat. (why seat instead of street)

By the shi... room with reek replete (maybe a reference to a place where the junkies hang out and which smells awful)
Crankin' an' a-coke'n
Out of his mind drinking a coke (??)

These are references to two specific [illegal] drugs. (i.e., using crank and using cocaine)
Valiant effort...

There was not much English there to work with :-)
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 Avangi's reply was promoted to an answer.
There are more drug-references here than you realise.
"Crankin' an' a-coke'n" -- "Crank" is another slang word for Crystal Methamphetamine.
"Coke" would be Cocaine, another stimulant -- hence four days without sleep.

"Green hocker croakin'" -- see also Mount Wannahockaloogie ("Finding Nemo" -- Pixar)
Indicates the poor health of a person "Crankin' an' a-coke'n", "On a four-day run",
"Hurtin' for sleep", etc.

Winchell's Donuts can refer either to a specific place http://www.winchells.com

or any all-night diner were people in the afore-described condition are wont to land.

"Joined the bus on the 33rd seat
By the doo-doo room with the reek replete"

"On the Bus" refers to a world in itself with reference to life "on the Road" with the Mothers of Invention. The reference dates to at least "200 Motels" (1971) if not earlier.

"This movie is about 'the Road'. 'The Road' will make you kRaZy." -- Ringo Starr

"On the Bus" is a significant quote from "Mary" (Dale Bozzio) in Frank Zappa's "Joe's Garage".
The complete quote is, "Thanks, now I can go home. On the Bus." Indicating that she has no intention of going home, or that "home" is, in fact "On the Bus". Mary was "stuck to Seat 38 on Phydeaux III"

Seats 33-38 are undoubtedly near the restroom at the back of the bus.

Phrases like, "Green hocker in a Greyhound locker" may be used primarily for poetic value.
You must realize that the song is meant to be performed so fast that the words are spoken almost as rapidly as humanly possible.

It was just the way Frank did things.
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