Before I go any further, I will mention this: when in doubt, and when possible, stick a 'Save Game' button of some kind in the sidebar.
I feel like I've been in this boat before with TFLights, and given that I'm now (over a year later) firmly of the opinion that I need to rip it out and rework... well, everything, that means that if my interactive stories do what my linear novels do when I re-write them, it's going to explode and triple (or quadruple) in length, which means re-working the layout as well as the storyline will be necessary, because the current layout would be a mess.
But forget I mentioned TFLights for now, because I'm going to talk about The Red Bandit. (It's a much better example than the messy TFLights.) TRB switches between Events that trigger based on the Day, Time, and other variables, and Investigation, which is basically giving the player free run through the town as s/he tries to work out the mystery of the Red Bandit. It's also, plot-wise, grown to about two months long. So, not including all of the character passages, the town passages, the character creation stuff, and my "lab rooms"? It's already looking to be 100+ Passages. But, moving on...
While the main point of the game is to catch the Red Bandit (not an easy feat when he is very good at what he's doing and the town is on his side), at times, Events force the player to follow a scripted storyline whether they want to or not. In fact, the entire first day (0) is scripted, as is half of the second day (1). Players can choose on Day 0 whether to go to the inn or saloon first, but either way, basically the same thing will happen.
All of the Event coding/plot for any particular day is in one passage. This was achieved by virtue of three things: WordPad (because MSWord automatically changes these (") to the curly version, which breaks things, and also because I can color-code unlike Notepad, which tends to save my life, and ALSO because, as I'm sure you've noticed, Twine starts lagging something fierce if you go over about 100 words in a passage; it doesn't autosave, but then, I'm an author and a compulsive (ctrl + s) hitter anyway); a clear idea of what needs to be between Point A (whatever got the player to the passage) and Point B (where you want them to end up at the end of the passage) so you can work out a basic outline to work through as you code; and a perhaps slightly unhealthy addiction to (click-replace:) and (click:)[(reveal:)[macros]] and |hidden)[hooks].
I'm not saying my method is perfect (far from it, since I usually have to copy-past into Twine and then chase down missing hook-ends, though it's become less common with practice), but it does help greatly for reducing passage numbers and the clutter that 100+ passages can make of a Twine screen.
And for cases where a decision affects the next segment of story?
Blah blah story~
|Where_Sit>[Where do you sit?
(replace: ?Where_Sit)[You sit in Place A.]
(set: $Seat to "Place A")]
(replace: ?Where_Sit)[You sit in Place B.]
(set: $Seat to "Place B")]
(replace: ?Where_Sit)[You sit in Place C.]
(set: $Seat to "Place C")]
(replace: ?Where_Sit)[You sit in Place D]
(set: $Seat to "Place D")]
|Chat_Time)[Blah, blah, more story text...]
I've stripped out all of the Story-related stuff (hook names, story text, etc.), but this section is already written and exists in TRB, and depending on where the player sits? They can get an opinion point for the single most difficult character to raise opinion points for in the game--the Red Bandit himself.
(Mind, you may need to play around with line break removers ( \ ) because I adjusted the coding to be easier to read just now. Might need to go back and do some tweaking on this story, too, but at least it's minor.)
I hope this helps at least a little. I know fighting with a LOT of passages can be difficult (TRB is at 121 at the moment, but that's mostly Character passages and Town passages), so anything that can collapse a dozen or so passages into one can help clear the clutter up some and make it a little easier to see what you're working with overall.
(Also, apologies, but brevity is not my greatest skill.)