Each of those subjects need to be examined separately from one another, as each one has a different origin and construct. For morality, Jonathan Haidt, an associate professor of psychology at the University of Virginia, decribed it as a cultural construct based on and restricted by a set of evolved psychological systems.
In an article published in Science Daily (University of Virginia. "Revealing The Origins Of Morality -- Good And Evil, Liberal And Conservative." ScienceDaily 18 May 2007. 12 January 2009), Haidt examined the differences between political liberals and conservatives and discovered that both groups built their morality upon emotional sensitivities to harm and fairness. However, conservatives also added three other constructs: emotional sensitivities to in-group boundaries, authority, and spiritual purity.
"We all start off with the same evolved moral capacities, but then we each learn only a subset of the available human virtues and values. We often end up demonizing people with different political ideologies because of our inability to appreciate the moral motives operating on the other side of a conflict. We are surrounded by moral conflicts, on the personal level, the national level and the international level. The recent scientific advances in moral psychology can help explain why these conflicts are so passionate and so intractable. An understanding of moral psychology can also point to some new ways to bridge these divides, to appeal to hearts and minds on both sides of a conflict."
For an interesting counterpoint, Michel Foucault basically stated that there is no universal morality, and that values have no origins and therefore can never be universal. According to Foucault, ethics and morality are structures of knowledge put in place through power structures and violence at a specific point in time. Morality and ethics, therefore, are not universal but a history of the conflicts and dominance of ruling forces throughout history. As a result, the individual is unable to establish or change the course of this morality, the individual is given no choice.
In essence, history shapes humans, rather than humans shape history.
Now, this viewpoint is strongly criticized by many, but it does offer another point of view to the concept of morality and ethics.
For emotions and thought, I'll leave those for now. Suffice to say, there are plenty of scientists out there that have examined both of those in detail, and there are likely quite a few studies that you could find on those. Be sure to check out the cited sources in those studies as well, as they will likely have alternate points of view that should expand your own personal definitions.