One technique I sometimes use is to turn on a 50% duty cycle PWM pin, and hook that to the input I'm testing.
May be a bit fast for this application, but at least it will show transitions.
That is a good idea AWOL, use the Arduino to generate a pulse. Or a 555 astable circuit set the the frequency you want. Or a second Ardiuno. That way, it will check the "counter program""
I am interest in this topic because it can be use a way to measure RPM ( ex : on a fan - using LED, Laser LED , IFR LEd ) or frequency counter. I will look at the "Sampling Routine" how you do it.
PS : This Forum is an exellent place to share ideas.