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One thing to note is that IR seems to have broken at some point between v0.45.0 and the latest on 3DS, it still works on DSi but on 3DS it doesn't work even for G5 Pokémon on the latest.
The Pokéwalker also did sometimes work on very old versions of bootstrap (the issue I linked above probably has some working versions), however it may be tricky to get working now as TWiLight Menu++ disables the Slot-1 card to save battery and prevent some issues. Your best bet if you want to try that is to load your ROM from TWiLight to set the config right, then exit to the 3DS HOME Menu, load GodMode9i installed as a CIA, then load the old nds-bootstrap.nds from there (Boot file (Direct), not Bootstrap file)