Jagged edges from joining with boolean modifier

Are you sure that all vertices and edges match fine? Try removing doubles and apply rotation and scale to that mesh, also if you could share that topology so I can see if there is another kind of issue

Umm I dont know if you already solve this, but I Have those kind of problems when I use zbrush usually is because your object wasnt dynamesh prior to merging, and you only merge them together in their plain sculpt mode so you are not adding geo to the object but intersecting the geometry of both meshes, also boolean is horrible because you get ngons everywhere, thats why some geometry can collapse on itself like is doing in your picture. Probably blender works similar to the dynamesh in zbrush.