Storyteller wrote:ok, so not even cosmetic changes to ship interior then, based on systems. What about cargo and augmentations? Could I make a 'cargo run' mod, in a sector where you buy and sell various cargo from on beacon to another and must fend off space pirates?
See Captain's Edition on how it could be done. Seriously, Sleeper Service has done an excellent job with the game mechanics in organising cargo runs.
Could I build augmentations needed for different events?
Ditto. Custom augments that do nothing but add blue options is possible. They just can't do anything else.
and lastly, can I make it so you can go back to an earlier sector?
No, but you can make it so that you stay in the same "Sector Group" through the use of Crystal sectors. See FTL: Infinite and Captain's Edition Infinite for details.
But in those ones, you can reach the end of Sector 1 and then go through a hidden gate that takes you to the Hidden Sector, but the difficulty will still be Sector 1.
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What I could also suggest is that if you're planning on a Cargo Run mod by any perchance, is that you turn the Drone Bay into a Cargo Hold and make cargo into Drones that you can sell at stores (and script events so that they do different things). The Drones don't do anything on their own so it's best not to launch them and waste the parts (or turn them into crew drones that resemble crates).