So after an unexpected session where the Rogue Trader TPKd the party followed by being torn into the warp. Seriously, all the player. I didnt even pick up dice.

The party restarts with people claiming new characters in order of death, they end up with:

Rogue Trader: Reaver Captain with ties to Dark Eldar

Kabalite Warrior: Dark Eldar who acts as second mate and Seneschal

Arch Millitant: Drugged up Beserker with the social grace of a mallet

Void-Master: Sociopatic adrenaline junkie

Explorator: The most stable and reliable Mad Scientist on board

Given my standerd campaign would not suit the direction the players have seem to gone im thinking of putting together a 'Golden Age of Pirates' style game with secret moon bases, stealth boarding action and looting hidden ruins.

I was wondering if anyone had done this sort of campaign or any ideas to make running it easier.

You might really want to take a look at Black Crusade. It sounds like you have a great group to use a fusion of that system and RT. A game like that would be great as a Black Crusade sort of theme. If they don't want to be 'Heroes of Chaos' on their way to becoming Chaos Spawn, you could probably just use the PF rules. The latest book for Black Crusade actually covers pirate groups among chaos pretty well.

That was my original thought, but then none are chaos. Just very bad people. And obsessed with monertary gain, one even wrote a page of back story about his characters obsession with money.

I dont yet have Tome of Excess as its not on PDF download but is it good for ideas of pirates and adventure? Or mearly supply pirate stats like Hostile Acquisitions?

If your captain is a Reaver captain with ties to Dark Eldar and you have Dark Eldar as part of your crew, you are pretty going to be lumped in with Chaos no matter what you try. Reavers are treated just like the actual Chaos pirates out there. Most of them are Chaos desciples. They are not going to be able to go as far as Port Wander without being the target of a variety of Imperial organizations and even other RTs. The players are not so much playing Rogue Traders as they are Pirates. They will need safe places to sell loot, slaves, and salvage to buy repairs/guns/drugs/slaves. Footfall might be safe…maybe. At least until an assassin or Inquisitor decides that you have become enough of a threat to have you removed, or the Imperial Navy visits your ships. Pirates are just as hated by those RTs who are on the 'wrongish' side of Imperial Law. They are some of the people you are going to be preying upon. The best ports for pirates are either Inequity (Citadel of Skulls gives a great overview) or in the Screaming Vortex (Black Crusade).

Remember that psychopathic pirates are going to be drawn towards Khorne or Slanesh anyways. They are exactly the kind of people that the Chaos Gods recruit. As their reputation grows, you can expect the number of safe places in the expanse they can stop in at to shrink. Anyone who considers themselves part of the Imperium will shun or attack them, as well as their rivals and anyone they have preyed upon. Profit Factor is going to be less about holdings and contacts with various Imperial groups and more about reputation and ready cash/booty on hand. The Infamy mechanic is probably going to be more useful later on than PF anyways. They don't sound like they are going to be setting up mining colonies and recovering archeotech for the Ad Mech.

As for Tome of Excess, it has some fluff about the pirate lords in the Screaming Vortex with some personal examples and descriptions of the areas they congregate. If you are planning to use the Black Crusade character rules it would make sense ot pick up. Pirates are just a part of the book. It may help with helping to understand how Slanesh is going to seduce your pirates (and whom the Dark Eldar are hiding from). Have you given thought to how you are going to handle Corruption and Insanity in a game that sounds like there is going to be a lot of it? It sounds like it could be a fun game, but the RT framework may not work for some aspects. I would be interested in what ends up happening with it.

There's no reason why you have to turn to Chaos to be bad people in it to make money. The Dark Eldar have managed it for millennia.

Looking over your crew, you could propose the following idea. You need to acquire a new ship for your growing pirate's nest, and a bunch of slaves to sell to the Dark Eldar in order to cement your alliance with them. Invent a Rogue Trader who has recently acquired a Mining Colony or a small venture in the Expanse that is reasonably unguarded. Encourage your players to launch a series of raids to get them acquainted with space combat, test the limits of how far they're prepared to go and then steal key infrastructure and supplies from the colony, but leave it invariably intact.

The Rogue Trader you're targetting will eventually notice this, and in fear of looking weak will arrive to try and take care of it. Before that happens, your Mad Arch-Heretek comes up with a home-grown toxin that will paralyze anyone who breathes it in for the next certain amount of time. You'll have to mount an expedition of your own to a Death World in order to secure the plant/animal that creates this toxin, but once you have it you'll be able to use the supplies you got from the mining colony to refine it. When the Rogue Trader arrives in his cruiser, your ship makes a distraction assault while the Void Master flies an incredibly insane boarding run against the ship, where your crew has to gain access to the life support system and pump the toxin throughout the ship whlie plowing through the defense forces who seek to bar your way.

Once the toxin is vented and the crew is comatose, you capture all critical personnel and tell the menial workers that as long as they serve their new captain their lives will continue much as they have before. Of course they won't because you're going to sell them all into slavery, but by the time they figure it out it will be far too late.

Bam. You gain a ship, Dark Eldar gain new slaves, reputation cemented, no one has to build skull thrones.

Oddly enough I could write up that entire scenario as a Compact for Black Crusade as easily as a RT endeavor. I assume that your players are going to refuel/rearm/repair their ship in some pirate outpost (Inequity, Screaming Vortex, or Dark Eldar stronghold?). They obviously are not long going to be using Imperial facilities, or the facilities of the majority of Rogue Traders. They are going to need repairs and refits that can't just be done hovering over some mining colony. They are going to need weapons and munitions that require a real industry to produce. There aren't a lot of places to get such things in the Expanse, and working with the Dark Eldar and being pirates is going to drastically reduce their options. Most of those who will deal with that kind of pirate are emeshed in Chaos. They are also going to need a running supply of slaves to keep their Dark Eldar allies (and crew member) happy. Raiding is probably the only way to do so over the long term. Any of the other pirate worlds have similar problems, and are home to major players of Chaos that are likely to try and draw successful pirates into their webs.

Their fall to Chaos is likely to be slow, but it is likely. It isn't the piracy, which is not all that uncommon among RTs. The toxin isn't even a form of Heresy, it is part of the normal job of the Ad Mech. It is the association with Dark Eldar, their own debased acts, and selling slaves to the Dark Eldar. Note that the Eldar fear Slanesh. They are hiding from him and in no way worship him…but he drains their souls away, and they refill them by debased and cruel acts. These acts are as vile and corrupting as anything a Chaos desciple does. They just have a different reason behind them. Significant interations with their society is going to gain you Corruption, just by going to their parties and making deals with them. Soul Reaver had a number of scenarios for players trying to emesh themselves into Dark Eldar society and, if I recall correctly, they tended to generate corruption among the players. While it is up to the GM to decide if Chaos takes an interest in the players, I would see it as very possible. As their corruption grows, they are going to be less able to deal in any way with the normal Imperium. Corruption is a measure of how tainted a person is. Selling shiploads of humans to the Dark Eldar is likely to leave its own marks on their souls. I could see a RT who wasn't associated with the Dark Eldar being a successful pirate and getting away with it for a long time before the Imperial Navy stepped on him, but that is far more likely when you tie yourself to the Dark Eldar or Chaos.

To make a different point, are they going to be looking for more ways to increase their power? Chaos offers a number of them that they can never hope to get through the Dark Eldar. Once you start dabbling in Sorcery, Daemon Weapons, and the warpcrafted items from the Screaming Vortex you start down the path of Chaos. The characters you described don't sound like they have a lot of self control, or any sort of moral compulsions. From a purely fluff perspective, they are allready empowering Khorne (bloodshed, berserking) and Slanesh (Excesses of many types). They could also end up drawing attention from Tzeentch (deception and crafty planning). They are going to be outside the Emporer's light as well. They may be able to find renegade navigators, but are they going to give up on Astropaths completely? If not, how do you keep a soul bound astropath serving a crew of Heretics? If they get more ships, where are they drawing the new Navigators from and how do they manage communications without astropaths? Do they hire Warp Guides (unsactions psykers/sorcerers that use demons and the warp to navigate)? Most games I have run with 'bad people willing to hurt anyone to make a profit' tend to slide down that slipper slope pretty fast. They can be fun, but I am not sure that the normal PF system really supports a pirate campaign like that. If nothing else, I would probably start with PF but plan on sliding into Infamy as they cut themselves off from the Imperium. Infamy is reasonably similar, and would work better with the Dark Eldar as well. Tome of Excess has some interesting uses for Infamy in buying pirate bases and connections as well. Just a couple pages of them, but I would take a really close look at them before importing them to use with PF.

However you decide to run it, it sounds like you can have a lot of fun with the game. Enjoy!