i just think its so weird that brookes would say that someone had visited the system.
Maybe prior to the introduction of permit locks? but if thats so that means raxxla is currently completely inacessible
That's misinformation, sadly, it's been investigated many times and it's just rumour and hearsay. Discard that from any thought processes because no-one knows who said it or when. There's some indication it was said at a Lavecon or something, but again, no proof.
Loved the read and your comments and made me stop and think 
So picking up on some of your thoughts and questions and here's some of mine in exchange
Awesome! Thanks for taking the time to reply
Searching for The Dark Wheel?
1. "Honestly I think we've already found the Dark Wheel home system, and the Dark Wheel itself. The confirmation is that we're told in the Codex entry that fake DW get shut down, and that hasn't happened to the Shinrarta faction (the exact opposite, actually)."
I can't really argue with this, however it doesn't mean Shin Rez is their home system?
However the search I am on is for the Dark Wheel base and/or how to get an invite to The Dark Wheel faction and visit the base legitimately.
If you believe any parts of the Codex then I guess you have to believe the others until it's ruled out as an option and as "the original group was based in a disused starport orbiting the eigth moon of an unamed gas giant. The station was toroid, hence the 'wheel', and operated with minimal power output so as to avoid detection, hence 'dark'" then it's their station I am looking for and rule out if there's any link to Raxxla...
I believe the Codex is basically a clue, intended as a story with hints - not 100% factual in every detail, it needs to be read and interpreted as any narrative should be. The whole section on Lyta Crane is, essentially, an
unreliable narrator's comments on what she
believes.
I think it's likely true that the Dark Wheel was named so due to a station, but nothing says the station is still where it was, or it's still the same as it was. If so you're looking for a 1000 year old station! I think it's incredibly likely that it's simply been moved and/or upgraded over the centuries ... say it's now Jameson Memorial, for example, (or inside it, since a 1000 year old station would surely be teeny tiny compared to a modern starport!).
The fact that there is a beacon mentioning the Dark Wheel around the 8th moon of a Gas Giant in Shinrarta is pretty conclusively close to the Codex - close enough for me to link the two. And who knows there
may be a dark station there too that we simply can't see.
2. "A while later you get awarded the rank of Elite by the Pilot's Federation (after much adventuring)..
Is your description how people gain access to Shin Rez who have to get access the intended way?
Is there a message players get mentioning Shin Rez and passing a test or do they just a permit added to their permit list?
This was answered earlier, so I'll just say that I think that general pattern is what a new player (even now) experiences, and I think it's structurally close enough to the method we know from the lore that it's probably what "being recruited by the Dark Wheel" means in the context of what the game can actually do.
4. "Personally, I think the Dark Wheel is a dead end anyway. All the lore says they were searching for Raxxla and never found it."
"To the jewel that burns on the brow of the mother of galaxies! To the whisperer in witchspace, the siren of the deepest void! The parent's grief, the lover's woe, and the yearning of our vagabond hearts. To Raxxla!
— Alleged toast of the Dark Wheel"
Is it directions to Raxxla? If so I guess they found it.... but then forgot how to decrypt it? ;-)
If not then you could be right...
That's a good point! I read the Codex entries as basically the same as all the myths IRL, they're a lot of hearsay and conjecture (Codex even references three such myths). Since this is a game and not real life though, I also assume there is a 'hidden truth' that's informing the Codex entries. Much like the Dark Wheel Codex I assume that the Toast is a clue or code, but it won't lead to Raxxla, simply to a 'next step'.
In the Lore we know for a fact that someone/someones/something has already found Raxxla and has apparently been using it for a long time. We're told basically the same thing in the Codex and original The Dark Wheel novella. I think that's one of the bits that's literally reporting the truth of the matter, Raxxla isn't a stargate sitting on a moon waiting for us to find. It'll be guarded and protected by someone/something that's actively stopping anyone else taking it over.
As I mentioned, I suspect that the problem with Raxxla isn't so much finding it as getting to it or using it (whatever that means) because of who/what is in control of it.
5. LFT 509 is permit locked by the PF, but so it Bellica, Alpha Hydri, Ross 354, Mingfu, Witch's Reach, and I'm sure many more... other than a galmap bug relating to star catalogue names I'm not seeing what makes LFT 509 more interesting than any of those others?
It may not be more interesting than any of the others but it's probably the most weird out of the bunch?
a) Missions you can't do...
b) Popping up as weird Thargoid attacks being around some of those you've listed and LFT 509...
c)The 8th Moon of a gas giant being a possibility based on the system information bought in game from carriers when FD hadn't blocked it...
d) That weird galaxy map bug... or is it...
e) Permit being reported as available by FD support? - "So it should be possible to obtain a system permit for LFT 509, but the permit holder and requisites are unknown" - Which kinda doesn't match what it says in game for the permits...
Or it's just a normal system in Elite Dangerous with some buggy code, bad support people, bad devs wasting time/money on developing missions customers can't enjoy, etc, etc... ;-)
Just some thoughts
Awesome

It may well be important
Most of us don't, this isn't a storyline, its something specifically put in game for us to solve and find, its supposed to be difficult and take years.
I am still of the opinion that Fdev hold the keys, once certain things have been discovered they will unlock access and to be fair it maybe one of those things we may be happy never to find.
O7
I think this is the case too. I also think they have a timer running (metaphorically) and if we haven't 'unlocked' it at certain points they drop more hints to help (like the Codex entries, which realistically they didn't
need to add at all), eventually if we haven't cracked it then they'll most likely drop bigger hints until it's solved. I think originally they'd intended that to happen at the 10-year mark (which matches Odysseus' journey in getting back home as I think is referenced in the DW Toast, and Brookes said there was a "ten year plan" for Elite, and this latest expansion being called "Odyssey" which will still be the title in the original 'year ten'). I suspect that's changed now due to Fdev issues and the pandemic altering things a lot - but it's likely still kicking around somewhere back there.