I recommend you open the IGS file in SpaceClaim. Go to the Workbench tab and click the Share button. This will create “Shared Topology”. When you mesh this in Mechanical, there will be shared nodes along the lines of intersection. Use this mesh in LS-Dyna.
I often use SpaceClaim and Mechanical to create a mesh for a Nastran solver. I use a Modal analysis. Click on the Mesh item in the Outline and in the Details window, on the line called Physics Preference, select Explicit. After you have meshed, click on the Modal branch of the Outline and on the Environment tab, use the Export Nastran File button.
I expect LS-Dyna can inport Nastran files. There may be a better way to move the mesh from Mechanical to LS-Dyna. If someone knows, they can reply.