Really digging this aesthetic, man! As far as the map glitch, no clue how to really fix it, but what if for each scene you had a counter for the number of "alive" enemies and kept their positions in memory and then loaded them back? I'm fairly certain you're on the right track here with the fact that loading the stack back probably brings them back to life. I think doing that essentially reloads the scene.
I'm assuming when someone hits the map button that triggers the stack save and you aren't saving it at scene load? I haven't looked too deeply in to stack save/load since for a turn based rpg with random encounters it doesn't really matter much.