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Certainly! With the work you all put in and the enjoyment I get out of playing, it only feels fair to repay it by engaging with you all here.

1) Yeah, I think it's a fair point that none of these three choice characters really get to shine yet. I picked Khenbish in my first run and was a little sad he didn't get to do a whole lot, but the homecooked meal was a super nice touch! And Themba is similar, but because he knew Asterion and provides insight that affects some dialogue later when thinking about P's grandfather, he feels more integrated even if he has the least scenes (No homecooked meal or second PoV chapter like Wolf). Oh and that reminds me that the artifacts you can find for the front desk/way you summon one as the Art background to get your 2nd choice in the list are genius. I felt it looked empty until you find one (or two), and it adds a lot getting to permanently see them as part of the background! Kudos on finding fun ways to showcase choices there (same with the restaurant screens).

Have you all considered how many days the player is going to get during the VN? Or well, it doesn't matter the exact number of days but rather how many things you want the player to see through to completion in a single playthrough in general. The MC has nearly infinite time, but the VN and main plot doesn't: you've mentioned multiple times that the player will not have enough time to do everything and learn everyone's stories/do everyone's sidequests in a single playthrough, which leans in to making the big choices matter more since more people will see all sides of them. I think that's a fair and important approach to take that leverages the VN medium, but maybe you're going to find you need to squeeze in more actions in a day to hit this number of completed things you're planning on having the player hit in an given run?
Looking at this build, you have I think 12 days to work with, with your options increasing over time. Luke's hangouts have 5 days (IIRC), Robert takes 4 to recruit, Asterion's project is infamously a 9 day affair that starts 3 days in, and that's not counting wanting to cook with Khenbish or manage assets with Themba to see how it works, get the flavor of them working, etc. If we give 5 hangout days for the other 5 staff members you can recruit in this build and count 1 day for seeing how Khenbish and Themba each work, that puts us at 45 days worth of content (and don't forget that it's about completion, so it's in chunks of 5, or basically 9 for Robert since you have to recruit him first). While part of the point is to have a lot of options, this many may already limit how many other things can pop up to take the MC's time - we already know of 3 new staff members for next build (even if only Leaders can get all 3), and there's still the Hydra we have concept art for and one other character hinted at in this build that could be staff, too (a certain book author that keeps popping up). 
Also, there is an opportunity cost letting a character be idle for the day instead of contributing to R&D or Exploration. We might see this more when there's a larger 'Tech tree' ready in R&D.

You all know what feels right with the number of things you want the player to complete in a run versus the number of days you have in the plot, but if you're feeling squeezed and think your average player will do 2, maybe 3 full playthroughs and worry the content would take 5 or 6 to see 'most' of it, perhaps you could move Hangouts to their own timeslot in the day? Maybe call it 'Grabbing lunch' with a character? Keep the opportunity cost of making them have an idle day off, but now I can grab lunch with Luke and start recruiting Robert on the same day. It frees up a lot more time for the MC, so you need to give them extra little things to burn their 'active' part of the day on or have slice-of-life events pop up that take this 'active' time away, but it doesn't feel too bad as the player to 'lose' a day since I'm still progressing with my staff during lunch time. This also ties into point 2, making the hangout with Luke (and others) feels a little more dynamic: chatting over lunch certainly feels relatively peaceful and a good place to just have a lot of conversation rather than movement if that's easier.

EDIT: Of course, this is more to plan for, more content to write, etc. Just wanted to throw out the idea since you've already mentioned having a hard time fitting certain things in that you wanted, sometimes things just have to be cut and stay on the cutting room floor.

3) Oh yeah, I know how finnicky moving around code and order of operations like that can be when you already wrote it one way, haha. Even moving up the selection would help I think, and if the system doesn't get shuffled around, I think you can still get a win if you just write the text a little differently to flow with what can't really change a lot.