My issue isn't really extracting or replacing music, that's simple, but rather modifying the game's code to copy channel 1 to the left speaker and channel 2 to the right speaker, instead of copying channel 1 to both speakers.
I've decompiled the game in Ghidra, but I couldn't dream of understanding assembly, so this is too much for me. I do know some things which are likely very helpful, though, if anybody wants to take this up:
1. Channel reference(?) is likely set per-file. So, every track's info table would have to be modified individually. I believe this is how it's done in games which use BCSARs, anyhow. Try feeding a stereo 3DS game a mono audio file and it goes berserk (literally just tested this with Devil Survivor 2 Record Breaker)
2. The game does output according to the 3DS audio setting, be it mono, stereo, or surround. Well I have no way of testing stereo, but it's safe to assume so. Surround effects DO apply to the game despite being mono, so the output mode isn't a hurdle at least. Therefor, it's same to assume that the only edits required are to the channels copied and where they're copied.
Anyhow, resources are provided to help, like a stereo audio file that replaces the title theme. Of course, in its current state, only the left channel is played.
bounty link: https://www.bountysource.com/issues/96492313-devil-survivor-overclocked-2-channel-music-playback