The SRL file you extracted from TWLN is not the same as the CXIs stored on CTR_NAND partition. They do not use xorpads as the encryption they use is different. I recall TWLTool can decrypt the encrypted amr7/9 sections of the SRL (as that's really the only encryption it uses besides the modcrypt part of the file).
If your thinking of modding the game, that's probably not possible at the moment due to RSA sig checks in TWL firm. No one has yet found a way to patch that out yet so modified DSiWare is currently a no go.
Otherwise the SRL you extracted from TWLN is ready to be built into a CIA. Or you can use a standard NDS rom tool to extract the game assets from it as I believe that part isn't encrypted or if it is, it's been broken a long time ago and the tools I know of do that for you.