I can imagine the frustration, cause I’m just wasting hours on the exact similar issue on a vast number of ornamental mosaic tiles, which come from AutoCad. There are times two vertices are connected by two segments, forming a closed shape and only single way to find out was looking at the yellow first vertices, blindly deleting the segment and finding out there is another segment just over it. Since it is closed, you can’t find out what is going on by moving vertices. I was almost going crazy, why two vertices in the same shape aren’t welding?
Only way seems to be doing it one by one, and to spare time, I narrow down the possible vertices by working in groups. I mean I select the entire vertices turn them to corner vertex type .
Show End Result button must be on in the modifier stack to see if the shape is extruded correctly. When I see the effect correct, I undo the operation and deselect a few vertices and try again until a problem vertices appear.
I wonder if STL Check works for splines, but yes, it might show the problems on the extruded model. It will eventually find several open edges though. Some other error type display might help.
Good luck and wish you patience.