When you clone a web part it will also create a copy of the files in cmswebparts.
By default it adds a "1" to the filename, but you can specify any name you want.

I'm guessing that since you use aspx templates, you could also copy the files yourself without having them registered in the cms (just like you would do with any other user control).

Hi,

You can also clone the web part simply by copying the source files and change their names and class inheritance in code behind. Then you need to register it Site Manager -> Development -> Web parts so the web part will be visible in the web part selection dialog.

Best Regards,
Juraj Ondrus