You should be able to run the browser exploit for running homebrew launcher which should allow you to run Emunand9Tool, Decrypt9, rxTools, CakesFW... anything you may want to run, really.
Through browserhax you can install menuhax to allow for offline access to homebrew launcher, and with CTRBootManager, you can autoboot directly into your preferred CFW (I use rxTools on O3DS, I heard Cakes was recommended over rxTools for N3DS but rxTools most of the important features work as intended on N3DS.)
Transferring saves you would have to back them up with svdt in homebrew launcher or SaveDataFiler, then restore them to your N3DS after re-installing the games. Sadly I do not think you can transfer save files for GBA VC or DSiWare so I hope you didn't have any of those installed with important save files you don't want to lose. That is, unless I'm wrong and someone can tell me how it would be done.
You play GBA games by either... well, N3DS can handle gpSP-libretro fairly well and I hear it runs the vast majority of GBA games full speed on N3DS, but otherwise you could use 3DS Simple GBA Converter to create GBA VC titles of any GBA game, and you can install those as .cia
You need to install them to both sysnand and emunand if you want to play them off emunand, or you can install them only to sysnand and run them from sysnand. In both cases they need to be on sysnand though.
On O3DS, rxTools patched AGB_FIRM on the fly, but that feature isn't supported on N3DS yet I don't think, and I don't think CakesFW supports it either. You will have to manually patch AGB_FIRM and install it over the old one using FBI to uninstall the old one and install the patched one in its place. You can use
this guide to do it. Be careful when deleting the old AGB_FIRM so you don't delete an important system title which may brick your 3DS.
(P.S.: patched AGB_FIRM must be installed to sysnand. I'm not sure if it needs to also be installed to emunand.)