Global initClockIRQ (void): The RTC interrupt isn't supported by the 3DS in DS or DSi modes. Any application that uses it will run on DS and DSi consoles, but not on 3DS. Also, most emulators don't support it either. The alternative is to use initClockIRQTimer(), which uses a timer interrupt instead.
Global keysCurrent (void): This function isn't safe. Normally scanKeys() reads the current state of the keys (from the ARM7 and ARM9) and saves the current state in an atomic way to prevent race conditions. keysCurrent() doesn't work in an atomic way, so it's likely to cause bugs. Use scanKeys() and keysHeld() instead.
Global rumbleInit (void): Use of peripheralSlot2Init() is recommended instead.