4) could also happen when you have been abused (or witnessed abuse) during your childhood.
Abuse can be any kind of traumatic event, even the most "innocuous" ones, like public shaming, ot when one of your parents suffers from a situation.
I'm a meditator, so all these processes are completely obvious and clear for me, since I witness them every day.
But even with the attitude of witness, I'm still sometimes a puppet of my own thoughts, so I believe that for untrained people, it's even harder.
About good and evil, believe me, good and evil are not innate, they are taught unconsciously, since our brain functions by analogy, or associations if you prefer.
For example, fear of altitudes, or vertigo, can be triggered by something totally unrelated to altitude (it's the same process as good and evil).
If something shocks us, it means that it hurts one of our self-identifications (you can call that our balance of good and evil).
It's really hard to understand which self-identification collides with the facts, and in my opinion, it's useless to explore, since there is no end to this exploration.
About intrusive thoughts (I didn't know this term), it's a normal process.
The real problem is that we associate our thoughts with ourselves, so when we have such thoughts, we tend to believe that we are wicked.
It's difficult to accept that these thoughts are independent from us (especially if you have a high IQ like I do, I believed that I was in control of my thoughts), so they give you a feeling of guilt.
Guilt disappears when you start searching from where the thoughts appear (yes, I'm meditating on this question, but didn't get an answer yet).