I've been trying to get this shape:

translate([0,0,tooth_bottom_zmax*0-.0001])
        linear_extrude(height = axial_face_width, scale =
tip_id/tip_od, twist=-gamma*0)
            scale([base_cone_r/rkf,base_cone_r/rkf,1])
                projection(cut=true)
                    translate([0,0,-tooth_bottom_zmax])
                        bevel_gear(*VARIABLES*);
to work, and it works on its own, but any boolean operation to it
breaks CGAL rendering and gives the error: "ERROR: CGAL error in
CGAL_Nef_polyhedron3(): CGAL ERROR: assertion violation! Expr: e_below
!= SHalfedge_handle() File:
/mxe/usr/x86_64-w64-mingw32.static.posix/include/CGAL/Nef_3/SNC_FM_decorator.h
Line: 426"

I tried using union with a cylinder(1,1) just to get it to do
something and it spits the error and just renders the cylinder.

This kind of error almost always means that something is subtly wrong
with a polyhedron or imported STL.

Try View/ Thrown Together, then F5 preview.  Carefully examine the model
for purple.  Any purple is bad.

If you supply the complete file, I'm happy to take a look.