tomsz,
I've attached a schematic that you can use as an interface for a universal counter. The Arduino has a built in counter. Use the pulseIn function. I suspect it's a legacy type function from when just about every counter used to work this way. Racal and Hewlett-Packard made a fortune selling these kind of counters.
When your first signal comes in it triggers the first flip-flop and the XOR output goes high. When the second signal comes in it triggers the second flip-flop and the XOR output goes low. Taking the clear function momentarially low resets the flip-flops. The LEDS give a quick visual readiness state.
You now have a universal time interval counter with near microsecond precision. BTW if you use other sensors you can use the same interface. You just need to get the flip-flops to trigger when you need them to without worrying about the Arduino.
