Oh well, this will be long... Some of your problems may already be solved, but we need to start somewhere...
Try to replace CTRtool in this package with the one from
this package. Most important, tell me if it works. Same for you,
@Haise
You know that you need to be running CFW for the injected H&S app to work?
Check the Decrypt9 thread (my signature). Decrypt9 now has an official readme detailing all the entry points.
EmuNAND ready does mean that your SD card is ready for EmuNAND but does not have EmuNAND set up. Does your EmuNAND actually work?