The biggest problem I've had is figuring out which events are the work of the Golden Fang and which are the work of the Feds, or even both if that's the case (if the Golden Fang is just a machination of the Feds to control hippie culture).
Instead of trying to chronologically detail what happens in the movie, I'm going to try to give a basic summary of each "story arc" and hopefully draw connections there.
So, the Golden Fang is this heroin cartel operating off a schooner with the same name, distributing drugs to LA hippies, who eventually turn themselves in, or are otherwise forced in, to the Fang-owned Chryskolodon institute to get clean, which also has a dental department to fix their drug-rotted teeth. They use hippies as a sort of triple income source, but they also seem to use strong anti-communist messages in rehabilitation. Could be a deal struck with the Feds, if the Golden Fang is not in fact a department of the Feds themselves.
Adrian Prussia is a high-end Golden Fang operative who also works as a sort of hitman for the LAPD, knocking off whoever they need and getting off scot-free each time. One of these hits happened to be LAPD Detective Vincent Indelicato, Bigfoot's partner, and very possibly partner. I'm under the assumption that Vincent was sticking his nose into the conspiracy and needed to be dealt with, but someone can correct me on that. Bigfoot has had a hard time dealing with this, becoming a pariah at the LAPD, which is why he sort of loses it in the end and decides to not-so-honestly lead Doc to Adrian's doorstep (when Doc is asking Bigfoot about Coy Harlingen, Bigfoot decides to lead him to Puck, and thus to Prussia), knowing Doc would kill Adrian, or at least try. When Doc screams hysterically at Bigfoot after he's killed both Adrian and Puck, Bigfoot responds dryly something to the effect of "I wasn't worried, I've seen you at the range".
Puck Beaverton, the guy with the swastika on his face, is Adrian's right-hand man; also the bodyguard of Mickey Wolfmann who was supposed to be guarding him when he was kidnapped. Instead, he switched places with Clancy Charlock (the dead man Doc wakes up next to) at the last minute, which implies his prior knowledge to the kidnapping. Bigfoot claims he's the guy who gave Coy the "fatal dose" that didn't really kill him.
Now who kidnapped Mickey Wolfmann and why? This is a confusing one. We know from the paper headlines and narration that the Feds want to use Mickey, a huge real estate bigwig, as a key non-Italian competitor to the monopoly the Italians have on the Vegas Casinos, but they are worried about his increasingly liberal ideals as of late. I think his kidnapping has something, at least allegorically, to do with Sauncho's (Benicio Del Toro) story about the actor who was blacklisted for communism, left on the boat Preserved (which was gutted and turned into the Golden Fang schooner), miraculously returned to Hollywood as a anti-communist propaganda actor sometime later, likely having been brainwashed somehow.
I think this is what was happening to Mickey, because he was planning to start embracing hippie ideals and giving his money away - most likely the influence of his love for Shasta - but the powers that be decided to stop him. When Doc pulls up at Channel View Estates we see a mass exodus of Aryan bikers - supposedly the group that's always guarding Mickey - and another group discreetly sneaking up on the building from the desert. I'd guess that the Brotherhood - probably in cahoots now with higher powers and disenchanted with Mickey's strange new behavior - left Mickey behind with the aforementioned Clancy Charlock, knowing these approaching operatives would approach and kill Clancy, kidnap Mickey. These operatives, whether of the Golden Fang or Fed variety, would drug Mickey, and take him to the Chryskolodon institute to reformat his ideals. It's there he insists to Doc, in a drug-hazed state, that his behavior was just some sort of bad hippie dream, but when Shasta's name is brought up, you can tell Mickey remembers something, and it disturbs him. I can only assume he really was in love with Shasta, despite treating her unkindly, and I think someone mentions as much at some point, to Doc's chagrin
Owen Wilson's character, Coy, decided to work undercover for the Feds to "do something good for the country" (I'm pretty sure, but not positive, that he was required to fake his death to go undercover), probably wanting to solve the rampant drug problem due to his own drug-addled past, but found himself way in over his head and missing his family, realizing the work didn't fit his ideals and that he's just "being used." He's an undercover snitch infiltrating his old group of friends, members and groupies of the surfer band The Boards, who are too doped up to recognize him (having supposed to be dead by overdose). You'll notice this group is mingling with the Aryan brotherhood at the creepy house party. So there's a connection.
