4b-1. Disadvantages: Trouble
Compulsive Obsession:
Both Shirou Emiya and Sengo Muramasa are individuals defined by their obsessive natures -- a single-minded pursuit of one goal. This kind of behavior has only been compounded by their fusion, as Muramasa slaves tirelessly despite his earnest and kind nature, to create his perfect sword. To hone his perfect technique. It's possible that this very obsession is what causes him to create demon swords rather than the pure divine blade he wishes for.  While aspects of Shirou's personality tempered Muramasa, it's not as if he didn't have his own quirks. Their lives and mindsets were 'incredibly similar' after all, so one of them being a twisted person would mean the other should be, too.

4b-2. Disadvantages: Significant
Hero of Justice:
 Shirou Emiya wanted to be a hero who could save everyone; of course, he knew that was impossible. But it didn't matter if it wasn't possible to do so, it's never about what's at the end of the road -- what mattered to Shirou Emiya was the road he walked on to begin with. This warped perspective still exists within Saber as a compulsion to make himself helpful, above and beyond what would be reasonable. If he can save even one life by putting his own on the line, he will do so regardless of his situation. In other words, Shirou Emiya's mentality pairs badly with Muramasa's obsessive desires in the worst ways, and has only served to push others away from him in the time he's become his current self.

Evaporation of Piety:
In relation to his desire for severing himself from fate, Muramasa despises the greater powers. The old gods who vanishes long ago, Gaia, even Alaya -- as ironic as that is -- his desire to create his perfect Muramasa comes from the deeper wish to escape the influence of others and act purely on his own willpower. In this way, you could say that Shirou Emiya's optimism and determination to carry through an impossible, eternal dream has improved his condition, turning what would ordinarily be a crippling mental deficiency into something relatively manageable.

Women:
Shirou Emiya was simultaneously horrible and amazing when it came to the women in his life. After all, how could he ever believe someone would love him? As someone who didn't value his own self at all, it didn't make sense for others to care for something that had no intrinsic value. Sengo Muramasa had no such problem in life, but fusing with Shirou Emiya has made it a very complicated affair for both of them, leaving Saber torn between Sengo Muramasa's long dead family and Shirou Emiya's tragically complicated love life. Sadly, even being influenced by a family man isn't enough to make his interactions with the fairer sex any less disastrous.

Yamato-damashii:
As a Japanese Heroic Spirit, Sengo Muramasa takes pride in representing his home -- a simple blacksmith manifesting as a Servant is a great honor, indeed. And while his nature is to an extent, humble, he comes from a time where the cultural values of Japanese men ran strong. Even someone as gentle and cultured as himself is no different. Almost always, he does his best to live up to the standards of the Muromachi period; to live honorably, and lawfully. His mental deficiencies in this regard make jabs at his roots incredibly effective in provoking him into fights he otherwise would try and talk his way out of. It's only natural to defend your honor and the honor of your contrymen, after all, at least that's how Sengo Muramasa would see things.