1. Yes I am sure they are .cia files. I tried running the sunshell .3dsx file and did all the instructions in the read me file but it would just give me a black screen, forcing me to reboot.
2. I'm not sure what you mean by CFW setup, but I am running Luma3DS which was installed through Pichaxx.
3. There is only one official source I got those .cia files from, Github. But they haven't been updated so maybe that is it.