I have modded my 3DS so I can open up GodMode9 and whenever I put any cartridge in, I get the message "Game card init...

This may be because you have Secure Boot, or your BIOS does not support Legacy. It's more likely that Secure Boot is turned on which you will find by entering the BIOS menu. In the Boot menu of the BIOS, you will see Boot Mode: [UEFI]. If you try pushing enter if it doesn't show anything other than UEFI, turn off Secure Boot which is right below it. Then try changing it.