Only refer to nodes that are children of the node you have as root for the scene. Don't try to refer to a higher-level node from a leaf. Accessing with an absolute path isn't needed.
If you use setget anywhere in the script, and those setters set things on referenced nodes... you'll probably encounter the exact problem I had. Godot runs setters on export variables before _init and _ready... so this works around that by killing the setter early if _ready has never been called.
var is_ready = false
var setter_thing setget set_setter_thing
if not is_ready:
# whatever you need to do
# everything needed on ready
is_ready = true