There is no definite link between the arcs. Just hints and bits and pieces.
One small but interesting one i encountered in the new game. When you find a diary in the Blighted village and read it, it triggers the first of Shadowheart strange "magical" reactions, with her hands shaking and glowing. You also find a skeleton with ancient Shar helmet right there. And in the few written pieces of info the hiding Thay wizard kept you find that a group of "dark knights" visited and even attacked the village. Which very well could be dark justicars which... went into the Underdark, and so on. Then there are the paintings in the Grove of Druids and Selune fighting the dark - Shar forces. Then the desecrated Selune temple. And on and on.
I dont think we would get so much pointers toward Shar if she wasnt involved. And if she is, she is running things. She is a major primordial diety, not just another god and has used the dead three for her own ends before to kill Mystra no less and cause a whole sundering of the Universe. And she represented herself as another god, which i already said. The Ilsensine god of the mindflayers is said to just appeared out of nowhere at one time, after a duergar uprising that nearly destroyed them completely. What a coincidence.
