MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Ok, so I was able to figure it out. For anyone else having this problem in Simplify3D, here's how to fix it. to fix the holes in the thin walls, select "perimeters only" under external thin wall behavior. To fix the issue with the intersecting faces, go to Mesh, Separate connected surfaces.