Quick Update : Godot 4.5
Reassembled the project in Godot 4.5 from scratch. Created new project, added new folders then Copy/pasted assets plus did a few scene/signal links changes in the scripts and it works perfectly. For now I only have one directional light in there so it looks a bit dull.
There were some minor hiccups like extends class or materials not updated automatically so I have to "refresh" the scenes by closing-reopening the tab. Other than that so far 4.5 feels great.
I have restructured my scenes and refactored the codes by moving the codes/signals to only be within appropriate nodes. Now I can add or remove elements like start menu, levels, pause menu, cutscenes..etc. easier
I have also re-add my original mobile controller so now you have an option to play with desktop keyboard/mouse or with a mobile buttons control at the start of the game.
The goal is a 3D web game that player can play with their desktop or their phone. I have no experience exporting game to any media but I read it can be a challenge with some drawbacks. I will try to test export a demo to itchio when I finish level 1.