Interesting to see the heart beats of the engines.

That would be 960 rpm would be correct.  You are probably only noting on your measurements (sound I assume) the power pulses.  Remember this is a 4 stroke motor so you have 2 full revolutions (720 deg) per complete cycle.  You are not really seeing the intake cycle which is a full revolution just like the exhaust cycle that you hear.  

Now on the GS500E that is a twin cyclinder 4 stroke with a 180 deg crank.  That means when one piston is up the other is down.  you still have one power pulse per 720 deg or crank ration per cyclinder but the two cylinders are 180 deg out of phase so you should hear twice the exhaust pulses but they are close to each other (offset of only 1/4 of the full period between noises). so it is possible they may sound like one noise but actually be two pulses close together.

if you had a 360 deg crank  (like an XS650)  then the pulses are full 1/2 period apart and should be easier to hear.

If you used an accelerometer to measure the revs then you should be able to see the primary vibration as 1 time per rev rather than the 1 time per 2 revs you are seeing with sound.  For the GS500 the 180 phase offset adds complexity to the measurements of sound or accelerometer but you should be able to see the primary and secondary interactions.

NOTE:  you said GS500.  I am assuming this is the GS500E or F which was a twin and not the original GS500 which was a 4 cyclinder.

Yes that makes much more sense if the first graph is the GS500.  I was assuming the oposite only based on the order you stated them but I felt they should be reversed.  you can see the double hump each wide wave on the first graph.  that is your double pulse.

as far as apps the one I have played with is RPM Gauge by Javier Yanez.  it is free.  I won't say it is perfect because when you get a good muffler on a multi cylinder engine it struggles but it is fun to play with.