i am not sure about the spiritual aspect of our thought origins. I will leave that concept to others with more knowledge about it to comment on it.
I will say, though, that I have found that usually when I have anxiety or stress it means I need to examine how I am living and adjust accordingly. So, for example, I tend to listen to a lot of news on the radio when I am in the car. Occassionally I find myself thinking at other times during the day (as you suggested, often times when I first wake up) “Oh the world is going to hell in a handbasket” or I worry about a nuclear attack or things along that line. Before I know it, my whole day can be clouded from the anxiety of that thought. So I really examine where it may be coming from. Duh, I need to listen to some nice music in the car instead of all that negativity. So I change my habit and the anxiety goes by the wayside. Until the next time of course, from some other bad habit I am stuck in , usually.
I have been on the anxous-side my whole life. I finally figured it out. It is usually caused not so much by what I think, but rather by what I do. This is the complete opposite of what many therapists will tell you, but it works for me.