just 2 points to mention so far (will split them into separate comments)
1: when the separation procedure is triggered at the start, for me the right hand section doesn't move (even though the merge block is off and the thrusters are firing)
- i did some experimentation, and the right hand section just won't move if the thrusters are triggered prior to disabling the merge blocks, but will the other way round
- obviously you've done it the way you have because as soon as the merge blocks are shut off there are now 3 separate grids, so they need to be shut off after the thrusters and other things have been activated (still avoiding spoilers just in case people got too nosy :-))
- am guessing possibly the groups don't remain on the other grids which makes it even more fiddly
- if i'm being dumb and this is actually intentional so that the player must act to avoid a spectacular disaster then i apologise and retract :-)
- if not then i have found some ways to do it - but likely you will find a more elegant way!
- also if this is only happening to me then sorry for the false alarm and i shall simply feel special :-)

2: I have noticed that the font size is very small on some of the LCD signs, specifically the "Corner_LCD" signs used to name buildings - e.g. the Medbay and Barrack(s) in Ieram City.
- possibly this is a global setting you used to accommodate the text panels with larger blocks of text?
- i think this one is pretty easy to do with a find and replace in the sbs file (searching for "Corner_LCD_" returns only 60 matches, of which i think less than half have text assigned)
- based on my experimentation, at max size (10) you get a single line with 12 characters, and at 5 points you get 2 lines of 24 characters, which should cover all of them i think
- i guess most would also need the alignment set to center (maybe left for a few)

so that's my 2 things i noticed - i hope they are helpful rather than seeming like i'm finding flaws just to be petty! :-)

also, since this is a place for spoilers, i was rather surprised and moved by the ocean fairy tale :-)

a note about factions:
- So, is the intention that now we can't take possession of anything and everything? I am not exactly sure about all the details of block ownership, but it looks like the owner keeps ownership of a block even if it becomes part of another ship through merging - so the only way to take ownership is to hack and rebuild the block?
- So when i started i left the House of Sarekh (sorry it was the only way :-)) so i could join the empire, at which point i was able to access all their ships and stations, but i could not take ownership of many since they were all owned by the founder of the faction (if i did not join the empire i could not access their ships even though i had max reputation with them)
- If i kick the founder out i become the founder, but then all sorts of crazyiness ensues and most things become hostile to me
- I'm cool with how it is because it means there will need to be some effort to take possession of the big ships and stations, and there are also enough without an owner that it is possible to have a personal little fleet (i'm using the Investigator as my main ship with the AEF Dawn as muscle - although she got a little banged up in a battle, so i shall be heading back to where i found her since i think there was at least 1 other unowned ship there.....)

Anyway - figured that since factions are new and you singled it out as a feature which may have some eccentricities that i would volunteer what i have seen :-)

UPDATE: Just found somewhere it is significant. Since i had to leave the House of Sarekh to join the empire, my rep with all the houses is now terrible (was terrible with all the other ones anyway but leaving a faction resets your rep to the starting value and for all the houses that is currently set at -1000). Hence i can't access the Warden above the moon. Obviously there's ways to do it in game, but i will see if i can work out a lore friendly way for this to work - would be good to be able to play the system as one of the Houses, and have that affect access to ships and stations (since that can determine which GPS locations are revealed) - with the player able to grind their way in if they choose but that will affect faction relations as well. Anyway - definitely some possibilities, but for the moment i want to see inside this ship before i get some sleep so i suspect i shall be cracking out the angle grinder :-)

UPDATE 2: Also, discovered you can join a faction, kick the founder and then leave yourself, which destroys the faction. I destroyed (dissolved i guess lol) all the factions this way. That then leaves all grids owned by single NPCs who appear to be enemies with everyone - makes for some fun scenarios (e.g. head to the gate construction site and then dissolve the empire faction) :-)

FINAL UPDATE (maybe lol): So the above showed that you can leave and join any faction at any time, regardless of reputation. So to get onto the Warden i just left the empire (who remained at max reputation with me) and rejoined the House of Sarekh, who hated me lol. But now i am their leader (seems weird saying that to you lol :-))
So, in closing, factions are not currently a problem because they aren't properly enforced - but there is potential to do some cool stuff with them (if currently it's just watching ships who were allies moments ago shooting the hell out of eachother lol) :-)

And now i shall explore the Warden! (then sleep for 3 hours lol) :-)
That ship is phenomenal! Beautiful!
And now i have another GPS marker!
But no - i must sleep - lol
so yeah - factions ;-)

Ok - just a thought - inspired by a screen i just read where a prospective Lieutenant is being sent to the Infantry Academy.
So you know how the First Jump scenario has level transitions? Well i guess all that's happening is that it is loading a new world when the trigger is hit.
So, theoretically, you can make the jump gates actually be jump gates and connect your worlds together....
I guess you've probably already thought about this but i just wanted to mention it coz it's pretty cool.
Obviously in it's simplest form we couldn't take our specific ship through, so that kind of thing would need some thought - but just travelling between each system without quitting and starting a different game is a cool start
Anyway, i will stop waffling and will definitely have a play with the first jump to see if i can find the important hooks - and if we can save data which can be loaded into the new world then there some serious possibilities for some serious multi system immersive storytelling and empire building :-)

UPDATE: Ok, i had a look at the scripts for The First Jump - maybe not so easy to untangle the bits needed to even do a single path of connected levels, and travelling back and forth may not be possible at all.
But it was a lovely thought while the possibility was floating through my mind :-)

Hey man, thanks for all the feedback! I am in the process of moving and this has somewhat limited my gametime ^^

The input about the factions is going to help me significantly, awesome stuff!

The seperation sequence for the ship used to work for the longest time, something Keen has done to the unmerging has bugged this -.- I will see what can be done about it.

The LCD corners: Keen changed that for some reason two releases ago and I could not be bothered to reset all the corners - but I might try the fix you suggested!

Right now, however, I am fully immersed in making a water version of my worlds with that new mod ^^

hey! - for some reason steam didn't subscribe me to the discussion, even though for a while i was the whole discussion :-)

glad the input is helpful and yeah, i figured they were all results of updates - hopefully my suggestion for the simple fix for the text panels works - and yeah, the unmerge only got me once (blew up half the ship lol), but i would hate for people to have it happen and then give up and miss out on the adventures! :-) (although if they give up that easily then that's their mistake lol ;-))

and right there with you on the water mod - just tried it today and Jakaria is pretty much the god of environmental mods with his weather and now his water (and if you're having a headache working out how to get a submarine to submerge and descend properly, since we can't drain tanks, i left a method on the comments page for the mod - but if you know a better one or a mod to drain tanks do let me know :-))

i still plan to go around the whole of Ieram system and get all the ships in a state so that if i enable the Orbiter gravity mod they don't all crash! (might even see about getting everything orbiting nicely)

So yeah - good to hear from you, and best of luck with the move, and i hope you get some more time to enjoy this golden age of mods that we are in :-)

(and i can't wait to see what magic you can weave with water on a world - i shall pack my scuba suit ;-))