Narcissistic personality disorder aka PRIDE might also be involved. I've encountered people who were reprimanded by the pastor and even those close to them but they would self-justify by saying they've prayed over the matter and decided that the priest and others are wrong. Probably they've never heard of this thing called malformed consciences.
Unquestioning obedience to your Confessor is the only real cure for scruples. I struggled with scruples myself (not to the extent OP describes), but to the point that I was always wondering if I was in mortal sin. That's a common condition when various thoughts pop into your head and you're confused about whether there was consent. In any case, my Confessor ordered me that unless I could basically swear to him that I had committed a mortal sin, I was not to refrain from Holy Communion and I was not to confess it as mortal sin. He told me that if I was mistaken, then the fault would lie with him and not me, and that God wants obedience more than anything else. So once you reconcile yourself to this mentality, to let your Confessor's judgment trump your own judgment, instead of always second-guessing him, that'll put your conscience at peace.
Now, I'm not talking about theological disputes, where it's OK for an individual Catholic to disagree with a priest, since this Crisis hasn't been sorted out by the Church ... but about internal forum matters and the application of moral theology.