Thank you for responding. Yes, I did activate the plugin and it appears. But I actually found something that seemed to fix it. All I had to do was put this line in my customnode.gd file. The line is: classname CustomNode. This wasn't in the guides and tutorials I was using, I saw class_name class for defining classes and thought it might work for this custom node as well and it worked!
Now the class is recognized it when I put in the code: CustomNode.new()
Maybe this solution is obvious for some people, but not for me.