Are your hateful 'thoughts' physical?
On the question of spirit, my definition is energy and I believe all combined non-physical aspects of self are spirit. You are disputing this. What is your idea of spirit?
You seem to be confusing processes with physical things. If thoughts and so forth are processes occurring in a physical setting (like a brain), it makes no sense to talk of them as substances, physical or otherwise. I suspect that this error is at the root of notions of "spirit" and "soul".
In a conversation recorded among Richard Dawkins, Sam Harris, Daniel Dennett and Christopher Hitchens (you can find it on Dawkin's web site), a useful distinction came up: spiritual vs numinous. Numinous has to do with feelings such as wonder that occur to people. Such feelings are real experiences, but any connection to anything spiritual (non-material, gods, ghosts etc) has to justified separately.