Create an invert for a mould

[micheus]

The original .obj file should have been saved tessellated as quads.

This should be the right file to work with. Although, one of those issue I found is already on the top of the sphere. That part would need to be rebuilt, but it's a very simple fix.

I wonder if it may have gotten worse by being cut in half by the Prusa slicer and saved as STL.

That would explain the amount of malformed faces in the project file you first shared. Too much conversion in the process.

The best practice would be work in the main project always. If you need to cut it in half section that can be done just before to export and than undo.
When the model has the correct shape then you can make the cut permanent.

Probably the boolean operations would work better in this scenario, although it's not infallible. Mainly because of that high detailed sphere.