Ok then you SHOULD just need to purge the extdata from your sd card. If I remember correctly you just need to load up the SD card on your PC and delete the "extdata" folder from inside the Nintendo 3DS folder.
If you already unlinked your NANDs then you will have two folders inside "sd:\Nintendo 3DS\". One is for your emunand and the other for your sysnand. If you are sure which is which, then delete the following folder and its contents:
sd:\Nintendo 3DS\<id0>\<id1>\extdata\00000000\000002cd\
<id0> and <id1> refer to the long unique strings of characters that are used for the folder names. If you are unsure which folder is your emunand, just delete it from both, but be prepared to set up menuhax again on your sysnand. Easiest way to tell which is which is to check the size of the two folders inside "sd:\Nintendo 3DS\". Assuming you have a game or two installed already, the folder you want will be significantly larger than the other.
Btw, this assumes you have a USA system. If you have a EUR system the folder is 000002ce. For JPN systems it is 000002cc.
Every CFW that does not actively patch the AGB_FIRM (in otherwords everything except rxTools on the O3DS afaik) will need the patched AGB_FIRM installed to play injected GBA games. This needs to be installed to BOTH sysnand AND emunand (set destination to NAND if using FBI), as well as installing the games themselves to both sysnand and emunand (set destination to SD for the games if using FBI). The ten official Ambassador games do not require the patched AGB_FIRM, they simply need to be installed to both nands.