Examining the source (yes, sue me), I think I’ve identified another bug. Spoilers abound:
If, during Jun’s past life experience, you are *successful* in helping Jun and go to the “madman_laughs” label, the statement {*set jun_defeat_past “true”} doesn’t get executed. That statement only exists under the “petulant_child” thread, and I’m almost certain that this is an error. If it isn’t, then you need to explain in the text why your apparent success was actually a failure, because it sure isn’t obvious now… 
Some more general comments (also very spoilerly, based on reading the code):
It is, I think, too hard to get to the “Jun turns into a homicidal maniac” plot-line. There are two ways to activate this plotline, and both are hard to get (but for different reasons):
…* First, if you are enemies with Jun /and/ you choose to continue to the zoo: But in this case you are allies with Sem and I suspect that the vast majority of players in this scenario will chose this route as it looks more “interesting”. If you are in a romance (not with Sem) then your romantic interest gives you a cue to stay with the tour, but…
…* Second, if you have a Red score greater than 70, Jun will attempt to kill you in your room, after field trip even if you do go with Sem. But a Red score that high is pretty difficult to achieve – and this route leads to an automatic loss, as you can “win” the fight with Jun, but you have to kill her to do it, and that leads to you getting into deep trouble.
Given how important Jun is to the overall plot, my feeling is that there should be another way to explore this plotline that is easier to find. Perhaps have Jun manifest some physically dangerous (instead of the seething behavior he/she has exhibited up to this point) if the red score is between (say) 30-75 in the block of text prior to Sem offering to allow you to stay in his room? Or perhaps have “enemy Jun” start counter-pranking the PC. Yes, I know he/she does this if you steal her boyfriend for the dance, but I’m talking about outside of that specific interaction.
On the flip-side, if the player has a high red score /and/ is friends with Jun, there should be options that indicate that the player wants Jun to /use/ the memories of her past-self, at least to share insights about the Red with the PC. Here are a couple of ways in which this could be implemented:
…1) During the past life regression scene, allow the PC a chance to try to make a deal with past-Jun (“My past self was afraid of what you had become – but I’m not that person”). Obviously, current-Jun would react poorly to this, but perhaps the player & past-Jun can convince her that /she/ is in charge (true enough, for now) of their relationship and that therefore it is “safe” to explore this knowledge (not true, obviously).
…2) After the confrontation with Cael (with Jun, obviously), the PC should have an opportunity to point out that Jun /knows/ what past-Jun has setup and how it all works. Perhaps it is dangerous to re-awaken such a powerful past self, but… At least one person’s life hangs in the balance and likely far more than that – isn’t it worth the risk (probably not)?
In either case, the choosing one of these options wouldn’t have much of an impact on the current game, but might be useful / important in part 3 (and you may be planning on exploring these ideas in part 3 in any case).
There should be some /advantage/ to the player for dieing in Part 1 – there are loads and loads of /disadvantages/ (which is to be expected). The obvious choice here is the ghost that the PC can interact with (way back in 02_intro_pick_classes, if you choose to ghost hunt in your free time). There is already some different dialog here if you died – I would expand this and make the ghost an ally (of sorts). Perhaps the ghost could be useful in the Cael confrontation (by finding the research notes automatically)? Or maybe the ghost could be useful in the physical confrontations with Clay (& maybe Jun – a protector against “ghost-Jun”?)
Finally, there should be some way to utilize / exploit your (non-Sem / non-Jun) lover for advantage (mostly for Red players). Given the timing and flow of the game, the only reasonable spot for this is with Cael – perhaps your lover can be exploited to swap your test for someone else’s. This would be a one shot deal and (likely) ruin your relationship with them, as this makes someone /else/ fail the test that should have passed, but hey, that’s what Red people do, right?
