If anyone else has this issue - I fixed it thanks to Boogieboo6!
In my example I will use FW 6.1 since I went from 5.0.2 to 6.1.0 via SX OS 2.3 with Auto RCM enabled via SX OS.
***I recommend you make a backup before doing this: You never know!***
1) Download the 6.1.0 file update 3 times from the same source and named each archive "6.1a", "6.1b", "6.1c"
2) Make a folder titled "Firmware" in the root of your SD Card
3) Create a folder titled "FW 6.1" inside of the "Firmware" folder
4) In the "FW 6.1" folder; create 3 sub folders:
a) 6.1a
b) 6.1b
c) 6.1c
5) Extract the full contents of each archive you downloaded earlier to each respective folder
6) Boot up ChoiDujourNX and select the "FW 6.1" folder as the source folder
7) After that ChoiDujourNX should find all the required NCA files
8) Follow the on screen instructions and continue to update your firmware
**If the above doesn't work, you can try to FTP the FW files to your switch. Link2811 (below) transfered the FW files via FTP and it worked!
Note: For SX OS users that might be confused regarding the Auto RCM being enabled etc... I am using SX OS 2.3 with Auto RCM enabled via SX OS and it installed fine. When ChoiDujourNX has the waiting screen to reboot, I plugged in my USB cable to my phone (for payload injection) and switch and held the volume up button. Then I selected reboot now while holding the volume up button and it booted to the SX OS menu and from there you can select to boot custom firmware.
I hope this helps and a big thanks to Boogieboo6 and the other guys who initially helped me in my other thread regarding SX OS Auto RCM compatibility with ChoiDujourNX.
Cheers!