A couple of issues for the game.
1. Too many battles with too many high level or numerous enemies.
A key idea to keep in mind for this type of gameplay is less is more. The less enemies you have to fight, the easier it becomes to get through an area, thus encouraging exploration. Also, basic enemies likes slimes should be able to be defeated in one hit with a regular attack, while scaling this upwards with other enemies.
2. Hp vs Stamina, the priority has to be on the former.
Because this game relies on HP more than Stamina, most items should be focused on restoring HP above stamina, otherwise players will get into a death spiral where they can't go far enough into a game to make it to where they can explore anything. This kills the idea of engagement, since you're stuck in a loop of immobility.
3. Saving should not be penalized without just cause.
Unless there is a major story reason why a player cannot save anywhere, there is no reason that saving should not be allowed to be universal. Or, if saving is tied to a story element, a save point somewhere that is comfortable is necessary. Considering that this game is on a time limit, having a specialized zone in the battlefield where a player can save and then transport back to base whenever, even if only one way, would be advisable.
4. Stamina goals should be percent based.
Considering the amount of items in the game that revolve around stamina recover, monster attacks should deal percent based stamina damage, in this way a player hedges a bet on enemy engagement, as well as resource management.
5. Stamina warning color code.
As with HP, if you are going to have a stamina based system that codes endings, make sure that the player will see this by having the Stamina Bar change color the further it goes down, because if events trigger at a certain number and one isn't paying attention because skills are tied to it, then it can mean that players can get a bad ending without realizing it.
6. Bad Ending Tracker
If there is some way possible, I would suggest making a visible tracker for how close you come to a bad ending for those who might forget, or put the game down for a while. A recap via a mirror to let the players know what has happened to them every other day would be in keeping in line with the game's overall tone and theme.
7. Monster Encounter Tracker
If you are using RPG Maker then you can go ahead and use the Region ID to code where certain enemies appear and in what number. In this case, making it so that rubbees can be found around the honey tree, while more slimes can be found around the further end of the map would be best, since it could give players a chance to measure their engagement, while also balancing their choice for encounters.
8. In the Slime Encounter, there is still text for 'green' slime instead of purple.