Have you looked at the crank sensor voltage / scope trace at high RPM? Are you using the stock inductive sensor? Inductive sensors produce more voltage at high RPM and perhaps you are over driving the input.

Spacing the sensor out a bit would reduce voltage but the risk is losing steady signal during cranking.

As for the 60-2 and 36-1 wheels / RPM. The 36-1 should produce less voltage ( ? ) over the 60-2 at the same RPM giving the 36 more head room.