I'm trying to build your citra repo from the latest commit as of writing, and video_core fails to build with "error C2228: left of '.Value' must have class/struct/union" at line 206 of src\video_core\shader\shader.cpp. I've been able to compile the official repo just fine, but your repo fails for me every time.
I don't have a wii u anymore to test it myself, but if homebrews are not visible on the wii u menu I think you can press L + R + minus to open the plugin menu, there should be an option called "homebrews on wii u menu" or something similar
Or when your player dies, you can say in code, if enemy exists, do nothing, but if enemy does not exist, then create enemy at certain spot. (This would be a pain tho for lots of emeies)