haha yeah it can take a while... BUT here is a way to do more than one at once
Say you have i dunno 10 roms you wanna convert, drag and drop ALL OF THEM at the same time together on to ctrKeyGen.py to create ncchinfo.bin as you normally would with one.
Then continue the rest of the procedure, putting ncchinfo.bin on sd card etc etc. It'll still take forever but atleast you can do more than one at a time, assuming your sd card is big enough.
Yeah some cia games can be a pain in the arse... I'm looking at you pokemon! Unless you don't do any editing then it's fine i guess. I just play that as 3dz now cause the cia version gave me a headache. haha