In case the readme.txt was not very clear about where to place the 'boot9.bin' file, it goes in the main '3DS Simple CIA Converter v5.0' folder and not in the 'xorpads' subfolder. You do not need to place a second 'boot9.bin' in 'xorpads'. You also do not need to Create 'ncchinfo.bin' file beforehand; this step is redundant. Just go straight to Convert 3DS ROM to CIA after once you have the 'boot9.bin' & placing your 3DS files in the 'ROM' folder.
Another thing I found out is that you do not have to worry about extracting different boot9.bin files from separate 3DS systems. They're the exact same file as far as I could tell using winRAR to check CRC32 hash between both of my New 3DS units. I dunno if differences in firmware create different boot9.bin, but both of mine are on 11.6-0.39U firmware.
Edit : More clarification. You only need to extract just the 'boot9.bin' file and not the 'boot11.bin'. To create boot9.bin, press and hold the (Start) + (Select) + (X) buttons for a few seconds at start up when turning on your 3DS. If you keep holding this combination, you will be stuck at a blank screen. This is fine. Just let go of the buttons to enter into 3DS Home Menu. Restart the 3DS while holding (Start) to enter Luma Chainloader. Select GodMode9, go to SDCARD > boot9strap folder to check if 'boot9.bin' , 'boot11.bin' , and 'otp.bin' were created. This might take several attempts and restarts if these don't show up. You can delete these three after obtaining boot9.bin.