I tried to find a way to do something similar, but I wasn't able to discover a solution. I would like to use the built in automation system in Mac OS, but I was not able to see if Shark supports this. I think it would be very helpful to have automation for conversion purposes too.

There's a scripting utility called AutoIT for windows that would probably be useable for batching conversion, if the script were written or recorded to do something like open PunchCAD, import filexname.3ds file (I'm guessing that they wouldn't have to necessarily have sequential names, but I don't know what convention would apply to importing them sequentially, and to exporting using the same name with different attachment), select all, export as filexname.dwg, delete all, import filexname+1.3ds, select all, export as filexname+1.dwg, delete all, and so on. The entire import/select/export/delete sequence is accessible with keystrokes, and checkbox and folder options appear to default to previous use, so it should be doable.