There's a lot of terrible interpretations and misunderstandings of this song online. I'll break it down by line, and then at the end give an overview of the whole song.
** Virginia was a lot lizard from Fla
A "lot lizard" is a prostitute that solicits at truck stops. "FlA" is a reference to Florida.
** She has a compound fracture in the trunk.
A compound fracture is a bone that isn't cleanly broken, whether it broke skin or in multiple pieces - basically, a fracture that doesn't heal easily. In the literal sense, he's saying she has a broken pelvis, or broken back. I think people are misinterpreting this; I think he is saying she has 'skeletons in her closet, a phrase that means she has dark secrets (fracture = skeleton, trunk of a car = closet). It's a little sloppy but fits with the following lines, and is more a foreshadowing of her drug habit.
** started when she ran away
As in ran away from home, as a teenager, prostituting herself for money/drugs
** thumbs out on the interstate
Hitchhiking
** she hitched a ride to misery
Running away from home would lead to a downward spiral of despair
** Mr Whirly has a catastrophic incident
I don't know for sure, but I think Mr Whirly is an allusion to the Replacements song. The catastrophic incident would typically describe an accident that's life changing or fatal - the incident is developing a drug addiction
** he fell into a city by the bay
Specifically, San Francisco. The word 'fell' signifies that it wasn't intentional (as we soon find he's homeless)
** liquidated his estate
Sold all of his possessions
** now he sleeps up on the Haight
Referring to Haight-Ashbury, a neighborhood in San Francisco that was particularly big during the counterculture revolution in the 60s. Since he 'fell' and he sleeps 'on' and not 'in, we can infer he is homeless there
** panhandling misery
Begging for money to feed his addiction
** chorus
He gets high because he feels miserable, but he's miserable because he's addicted. He's past the point of no return, and although he yearns to find happiness that he once had, he knows its futile to try. Instead of nostalgia, his memories only serve to remind him how much his life sucks in the present. When people close to him are hurting, watching him crash and burn, they want to understand why it's happening and why it can't stop. But there isn't an answer, and it's nonsensical, but its the way it is.
** Vinny was a hustler of New Amsterdam
New Amsterdam is what New York City was originally known as. 'Hustler' could refer to a million things, but in this narrative he was likely selling drugs
** he ran a drug cartel in Tinseltown
He moved to LA and started selling drugs. Tinseltown refers to Hollywood. 'Cartel' is a bit hyperbolic, as its implied he's working solo...
** they found him in a Cadillac, bludgeoned by a baseball bat
Not really the death of a gang leader. Absolutely reasonable for low level dealer that crossed someone the wrong way
** in the name of misery
If you haven't caught on yet, misery means heroin. He was likely a heroin dealer in New York, moved to LA and kept selling but was impeding in someone else's turf, and was beaten to death. Well thats what it would be, unless...
** Gina hit the road to New York City
Hey, isn't that where Vinny is from?
** Mysteriously the night Vinny croaked
Hmm, maybe they're related?
** She stopped in Vegas to elope, with Virginia and the dope, and kissed the bride eternally
Eloping is running away to get married, and Vegas is a popular spot for impulsive elopement. This verse reintroduced our protagonist, and we know she is addicted to drugs, so this pulls everything together. The vague 'compound fracture in the trunk' may have actually been foreshadowing this incident. We know Gina and Virginia are lovers, considering they are running off to elope. Gina left the night Vinny died, they had a sum of drugs with them and were on the run. So what likely happened: Vinny may have been a pimp of Virginia, and may have also sold drugs ('hustler' alluding to that he has multiple illegal ways of making money), Virgina wanted to get out of prostitution and it wasn't as easy as saying I quit. Her and Gina formed a plan to run away - they would kill her pimp. Because he was killed with a bat inside his own car, it was likely someone he trusted, or at the very least didn't see as a threat. He was sneak attacked with a bat, Gina and Virginia stole his money, drug supply, and car - the 'compound fracture in the trunk' is his shattered body in the trunk of the car. They drove off into the sunset, high on love. And heroin.
** Hell hounds on your trail now once again, boy. It's groping on your leg until it sleeps
Billie Joe closes the chapter and goes into a more generalized narrative. Hell hounds are mythical beasts, essentially the service animals of Satan. If we understand heroin addiction as an entity leased out by Satan, where you would contract with Satan for the euphoria heroin brings, he sends in the hell hounds to enforce the contract - the hell hounds represents withdrawals, where when you stop you are hit with physical torment until you use again, when "it sleeps" until the high wears off again.
** the emptiness will fill your soul with sorrow
The cyclical nature of addiction completely sucks the life out of you. It comes to a point where there is nothing left, your only focus is getting high and figuring out where your next high is coming from. You don't have time or energy for anything else, so you lose everything that made you who you are- your hobbies, friends, dreams, aspirations... all gone. Its all drugs, all the time, and that's one of the darkest existential depressions one can slip into.
** its not what you make, it's what you leave
Life is no longer about creating, making memories, producing tangible artifacts, building families, etc. Instead, its leaving withdrawals, and leaving the depressing reality that you've trapped yourself into. Because when you're high, you can briefly avoid misery. Life isn't making happiness, it's leaving misery.
The whole song is about heroin addiction. It tries to demonstrate a gritty vignette of the throes of heroin through interrelated stories that tie into each other. I think Mr Whirley is just to paint the scene and build context. Its also possible that Gina and Virginia are the same person - Gina is a nickname for Virginia, and the elopement could just mean she was 'Eloping' with the heroin, in the sense that she was committing the rest of her life to it. Its emphasizing how it really destroys your entire life, and even trying to escape you will always be followed. Like the movie Requiem for a Dream, it's trying to show the misery of heroin addiction from the point of view of the addicted, but not first person; its trying to objectively describe it, because within addiction you can't always appreciate how destitute you really are.
It's a beautiful song, and it bothered me no meaning had done it justice.
