The system transfer process is mostly the same as it would be done without CFW on either device, but you will need to use faketik at the end to restore any applications and games that did not come from the eShop.
What You Need
The latest release of GodMode9 (the GodMode9 .zip file)
Copy GodMode9.firm from the GodMode9 .zip to the /luma/payloads/ folder on your SD card
Copy the gm9 folder from the GodMode9 .zip to the root of your SD card
Reinsert both SD cards into their respective consoles
Section II - NAND Backup
Creating a NAND backup of both consoles is a good idea in case something goes wrong. It ensures you can recover your data in the event of an error.
For both consoles, perform the following steps:
Press and hold Start, and while holding Start, power on your device. This will launch GodMode9
Press Home to bring up the action menu
Select "Scripts..."
Select "GM9Megascript"
Select "Backup Options"
Select "SysNAND Backup"
Press A to confirm
This process will take some time
If you get an error, make sure that you have at least 1.3GB of free space on your SD card
Press A to continue
Press B to return to the main menu
Select "Exit"
Press A to relock write permissions if prompted
Press and hold R, then press Start to power off your device
Insert the console's SD card into your computer
Copy <date>_<serialnumber>_sysnand_00.bin and <date>_<serialnumber>_sysnand_00.bin.sha from /gm9/out to a safe place on your computer, then delete both files from the SD card
Reinsert the SD card into its console
Section III - System Transfer
Perform the system transfer as usual. If at all possible, choose a "PC-Based Transfer"
If you cannot follow a PC-Based Transfer and must instead use a Wireless Transfer, be aware that with this method, homebrew software, cartridge dumps, and any other data only obtainable with CFW will not be transferred over. If you choose a Wireless Transfer anyway, you will need to take extra steps to move over the lost data.Select "Do not delete" during the transfer to preserve all data on the source system, or else you will have to reobtain all lost data again by hand.
Next Steps - Branching of the Way
Were you able to perform a PC-Based Transfer in Section III?