Setup J-K Flip-flop for logging on Arduino RESET
Rather than having events that set 1Q or 2Q, consider having the external events take 1R\ or 2R\ low, to reset 1Q or 2Q.  When your sketch starts up, it would read 1Q and 2Q.  If one or the other is low, its event occurred and you can log it.  Then the sketch sets both Q's by dropping the CP lines with J's wired high and K's wired low.  You'd use three I/O pins: two for reading 1Q and 2Q, one for strobing the CP lines to set the Q's after reading them.

Arduino AVR pins default to inputs on Reset so the Arduino can reset without affecting the 74HC73's state.  A 10 to 20KΩ resistor to passively pull the CP lines high is reasonable.

Edit: Note, 1R\ and 2R\ operate asynchronously, and are independent of clock inputs.  This leads to simpler interface requirements for your external events.  However, it may also increase sensitivity to electrical noise; if your system is in a noisy environment a different approach might be needed.