Sorry Tea Rex I can't make the quotes within quotes work!
What I am wondering is how you are handling the advanced technology of the ancients? Did you give them all achievements of a certain techlevel? And how do you do the balancing. My players tend to powergaming, so I always have to be very careful what I give to them.
(This is a long answer, but I hope worth it)>
SPOILERS for Secrets of the Ancient ahead BTW.
The ancient technology is kind of just there in the background. The ship they have is 2 million tons (an asteroid - look up Oumuamua in your web search engine of choice) and is really just a mobile base to come back to. They have decided to take a TL15 ship (still very nice) to visit planets so that nobody knows that they have such advanced tech available to them. It's most certainly power gaming, but for a reason. By taking some of the mundane things out of the equation (e.g. engineering and space limitations - the cargo bay is 1 km long and the power plant is a small sun with limitless fuel) it means they can concentrate on exploring, discovery and first contact, rather than the things they worried about in Drinax and Ancients.
As for how they got the ancient tech. For those familiar with the Ancients campaign the characters experience some of the memories of agents at the time of Grandfather - the players control agents from 300,000 or so years ago. A side effect is the ability to fluently speak Droyne (as the campaign puts it "...although the messages are in the Droyne language, all the characters appear to have gained the ability to speak Oynprith (a side effect of the telepathic flashbacks in the last adventure")). Near the end of the campaign there is a moment where Grandfather and his nemesis are vulnerable (or potentially so) and the players can come down on one side or the other. My players chose to side with Grandfather and after everything was done and they had escaped with him he had a conversation with them on the ship, only some of which the players themselves were party to at the time. Grandfather then left them, but before leaving he temporarily withheld memory of him surviving and the conversations they had had. The characters thought Grandfather to be dead.
Anyway, the characters went about their business trading and doing some wandering around but they kept noticing things about the Octagon Society everywhere they looked. For some reason it seemed important and they didn't know why. Being naturally inquisitive they followed up many leads, visited many places, and eventually found out that the planet they had been settled on following the Drinax campaign (like witness protection) had a hidden octagon tower, and under that, once they found it and explored it, was an Ancient base with a single working portal. The portal took them to a new Ancient base. This base looked very similar to the old D&D Barrier Peaks maps (hehe) and thanks to Jon Pintar (maps available on DriveThruRPG) I was able to set up the Fantasy Grounds table to take a Traveller party through Barrier Peaks, Vegepygmies became Chirpers, and I trawled through all the MgT material to find new animals to replace the D&D ones. It actually worked excellently - especially the little girl in the central white room who turned out to be the AI. Long story short, the players took a couple of years slowly working out how to fix the base, helped by droyne that popped through from some cloning facility to build up a workforce and family group.
The party could speak Droyne but I decided they could not read it, and the barefly functioning terminals in the library were in droyne written language. So the years that passed, were in part spent spending points learning the written language of the droyne to understand the manuals and instructions in front of them. I introduced "Engineering (ancient tech)" and "Science (ancient tech)" and "Electronics (ancient tech)" as skills to learn but they had to have the non Ancient versions at a higher level, and the written language at a higher level. Basically you had to build upon your common understanding, and use your grasp of the language, to work out how things worked, and therefore how to repair them (within reason).
When language got to 3 (it took a long time) I gave most of their points back and the 'ancient tech' skills went away. This represented them now many years later being conformable with the technology and the language. All in all I think the characters were on the base (hiding out from the rest of the universe) for four years. It was very comfortable, and they were learning cool new things. (plus it was somewhat fast-tracked as far as running the sessions was concerned).
In the middle somewhere Grandfather just popped in through a portal one day. He congratulated them on getting the base running "as they had agreed before he left them". When they looked blankly at him, he remembered that they did not remember, and freed up their brains. The backstory being that they had all discussed and agreed to go to the octagon tower on their home planet, go through the portal, and when all systems on the base were working Grandfather would be advised and he'd return to make them agents.
(Sorry for the long explanation, the shorter version should have been "they spend skill points understanding how things worked, and once competent, we moved on).
How exactly do you prepare for encounters along the way? How do your spreadsheets look like? It seems this could be also extremely helpful in my campaign.
I think this touches a very crucial point in running the campaign: The campaign is epic and tons of ideas and adventure seeds are to be found between the pages, but for such a long journey, this is still not enough. It is impossible to address every possibility and also improvisation has its limits. For example, at some point the letters and numbers in the spreadsheets of star systems fail to give you new ideas, but the players choose this system for general overhaul and you want to make their stay more interesting...
It's still early days. The first function of the spreadsheet at the moment is to mimic sectors and subsectors (using merged cells and drawn hex objects) with a formula in each randomly determining for normal and rift hexes whether there is a planet there or not. The second function is to randomly generate (as per Great Rift rules) the systems in terms of star(s) and their types, the planets, and that's about it. Creating formula to create a system which I can then copy and paste into another tab means I can generate random subsectors in no time. I do cheat and create maps for my Fantasy Grounds table in PowerPoint (saved as png) by having a number of hexes that I can match to the spreadsheet. If I can work out where to put some screenshots I'll add a new reply linking them.
I have not worked beyond the stuff in Riftsedge Transit but am noting down ideas for things the party encounter randomly in between all the bits in the other books. I'm expecting to not do a lot more to be honest as there's already a huge amount to get through without adding more. However by having a bunch of single paragraph ideas, and a means of generating the mechanics of the star system (some of which - most - will just be boring), the gaps can be filled quite easily. I also have up my sleeve Droyne scientists looking at the scan results and pointing out a half dozen potentially interesting systems for scientific research each time the arrive in a new area of space. And for clarity, it is perfectly ok to have boring systems all over the place. Not every place the party visits has to be interesting, and that makes the interesting one stand out more (as long as you don't torture the players..... too much).