Instinct, it seems to me, is a hardwired reflex or behavioral response, largely unconnected with reason. In fact, the less reason a being has, the more instinct seems to dominate.
Neuro-psychology I think of as an operating system, automatic, and personalized by culture and socialization.
Reason and logic are more formal, algorithmic devices. Mechanisms of analysis, planning and execution.
Instinct and emotion, unregulated by learned moral principles or social values, seek to benefit the individual without consideration of externalized consequences. In a society, they can be dangerous.
Hominens are hardwired to function optimally in small bands of hunter-gatherers. Psychologically we're intensely loyal to and supportive of our own band, but competitive with neighboring bands. Our altruism and moral universe is very narrow. Extending these to encompass a city-state or civilization is problematic. We're not naturally adapted to a civilized lifestyle. The requisite values and behaviors must be learned, and are only tenuously installed.