Going with how the game is, I see two ways.
You can either go the ChäoS;HEĀd NoAH route and make the VN format a "fandisc" that adds a metaplot to the already existing one, and use that to justify the new mechanics.
Or you can add a disclaimer at the beginning that specifies that you're playing the WRONG version of the game, because the affection and lust points are unnecesary now. Still, leave everything that could be avoided as a choice, which would actually make it more like a VN, and maybe add a computer option that tells you what to do if you haven't triggered an event after 7 days.
Either way, as you said, both involve renpy knowledge to at least change or patch Sel's one.
Ideally for the mod I have in mind, I want to keep the story as it is now but make navigating and the grind towards the events more enjoyable in a sense; the idea is to reduce the amount of grinding you'll have to do, assuming you not using cheats or URM to boost numbers, but also make the grind more enjoyable and interactive to deepen the connection a player might have with the character in the game, answering questions about them and Sensei, having conversations with them, small dates and if you really want to get twisted, make those events glitch out from time to time, have them know conversations from the future or the happy events, corrupt the characters and make them insane momentarily or hell you can even make
Ami Hiwamari appear in those events from time to time, it might add mystery, intrigue, arouse the curiosity in people to make them more invested in the game and the characters. Later on, you can have this events changed up to reflect the
corruption growth the characters have gone through.
But that's only one aspect of improvement you can focus on, as you might also want to improve the menus, the gallery and the navigation of menus; tell me how you're going to find a specific character within a main story event without being absolutely
demented dedicated to know them by heart, we can't always have Moonflare, Fdsasdf_p, Shmurder, Barglenarglezous or the other smarter members here remember them for us, I feel like having images or character mentions or maybe even a menu within the character's profile event gallery linking them to an main story event would make remembering events easier and make it more... I don't know the word for it easier to enter the game I guess?
And the difficulty of the dumb reset events oh my fucking god, you can do so much things in order to make the logic puzzles easier while also increasing in difficulty later if you wanted to, I'm not smart, I honestly wouldn't have passed the first reset without the wonderful members here making guides and walkthroughs for my pea-brain. Here's an idea, can't you have the souls/bodies of the previous Senseis stuck in the same room as they giving you small hints and insights of what events you need to review or what information you'll need to pass the lock and as you go on, since the Senseis get filtered out for being dumb as me, you get fewer Senseis to gives you hints as the loops go on and go on but you'll grow as player and be able to remember important information that might come up later in a loop event. FUCK anything in game that could give you hints or guidance to complete the event, don't we have gods whisper insane things in our heads during those events? Why don't you make them into a gameplay mechanic, they give you hints but in a insane/lunatic type of way making you have to think as fucked as the gods themselves and give you a point of reference for later events to understand their rumblings and insane speeches without having to decode them too deeply.
You can also improve on the lust events by making them animated but I'm not really sure if that'll work to interest players.
Cckerberos has already done a wonderful hint mod on what to do to progress the game and what events will lock out content so honestly there's no need for improvement on that aspect.
Sorry for the rumble everyone.
Amy*, and that one would be simple, there's 20 locations, make it a simple linear progression, 1>2>3>etc. and adjust for any inconsistencies, of which i don't think there are any, you can backtrack pretty easily in that event but if memory serves, they're just meaningless alternates, you wouldn't miss anything by just showing the initial version of each location.
Probably the easiest solution and the one I would probably use to streamline the event, even if it takes control away from the player, It'll make it easier just go through the event and seeing all the unique dialogue before you exit the event, the only real issue is a lot of reading in a weird atmosphere but I assume if you're already in this deep into the game, it would be normal to have events like this.