Hi, thanks for the in-depth critique and high praise, glad to see you enjoyed this version!
-I'll see about tweaking the timer in the sun sector so it doesn't keep running during dialogues, although I'll note there's a "secret" option that if you equip either the shadow or void magic item, when the timer runs out you'll be able to keep going, it should be hinted by the teacher.
-Speaking of hints, the space boulder event says it's brittle and needs brute force, the intended magic item to equip is the Mighty Amulet, what made you feel like it was the electricity item that was meant to be used (in particular since the electricity item is used to remove another nearby obstacle in the main space map)?
-For the neko vulnerabilities, they're coded to be resistant to Wood (they're actually Wood element themselves and use Wood magic), the student hint is that they're vulnerable to fire, frost (ice), toxins (poison is its own element) and machinery (most basic gun attacks are this).
-The healing items were definitely bugged, will fix them, thank you very much for pointing those out!
-Stat buffing may indeed be too strong, will tone it down a bit. And yes, the boss battle version gets some extra stealth buffs as allies are defeated, probably should make it more visible to make it fairer for the player so they can notice they're stronger than usual.
-I can see the argument that enemies have too much HP, will nerf that too.
Thanks once more, lots of great advice for me to work with!