I sliced the STL in v1.1.2 and from what I can tell, the G-Code looks correct. As you mentioned, there were several non-manifold issues, so you could potentially have problems if your specific choice of layer heights happened to coincide with one of those problem locations. If you want to post a .factory file (so it contains the STL and the FFF settings), I can probably provide more information on what's happening.
A non-manifold issue can be difficult to troubleshoot and many times requires actually modifying the original CAD model to fix it. The first thing I usually do is use Repair > Identify Non-Manifold Edges to actually find where the problem areas are. Then you can use the cross section tool (View > Cross Section) to hide parts of the model and zoom in on the problem area. After doing those steps I can already see quite a few issues with this model where you have overlapping or poorly formed triangles. Creator can attempt to remove overlapping triangles or help fix the orientation of adjacent surfaces, but it's usually much more effective to fix the problem with the original CAD model. In fact, there are many many scenarios where you won't have any other choice (since CAD can make theoretical shapes that are not possible in real life).
There's definitely some serious problems with the tiny triangle that sticks up at the very top, so that would be a good place to start!