Just patch the AGB_FIRM with this:
https://gbatemp.net/threads/release-agb_firm-signature-patcher-gba-rom-converter.390313/
I can't say much for making your own GBA .cias (shouldn't be hard though with the tools around), but once you patch the AGB_FIRM you can install the .cias right to your emuNAND (or sysNAND if you prefer, but I recommend emuNAND wholeheartedly for safety reasons) and you don't have to also have them installed on your sysNAND. They'll always boot you back to sysNAND when you exit though.
If you
really don't want to do that, though, check out the retroarch thread:
https://gbatemp.net/threads/retroarch-emulation-thread-nightly-builds-included.400913/
It lists which cores are best for which system. If none of the GBA emulators there are to your liking, mGBA is good (and I don't mean the one included in that thread), though I don't know if that's available as a .cia, nor do I know how to make it so.