Thanks! That about covers it.
So I'll just dump the roms over to the blue card. I'll play with save games and GBA emulators and try to get them working.
Any risk here of bricking the 3ds or messing up the GW exploit?
After using any DS mode card, you will need to reinstall the exploit using the blue card or any other compatible DS mode flash card. I suggest the latter, as the blue card is cheap as hell and has known compatibility issues with many games.