About the 'game card removed' error, I've managed to get around it.
I tried reformatting my 32GB Class 10 MicroSD (as FATex, because FAT32's 4GB limit is annoying) with no luck. But I dug out an old 4GB Class 4 MicroSD card I had lying around, formatted as FAT32 and copied only the Devmenu.3ds onto there, worked perfectly. From there, I installed Govanify's .cia version so I no longer need the .3ds file. Works fine.
jonthedit's note: The exFAT (or FATex as sj33 calls it) / FAT32 difference does not actually matter, but the card size DOES matter. It should be noted that this is the case.
No idea what the cause was, but that's how I got around it - using a separate FAT32-formatted card to install the .cia