The Arduino is only measuring the frequency of the square wave output which I convert to 0-5V with a transistor.
So is this translation simply for the arduino?
If so then there is no need to preserve the waveform, simply put it in the base of a transistor ( through a resistor ) and have the emitter to ground and the collector to a digital input. Enable the internal pull up resistors.
That will allow you to measure the frequency of much faster waveforms than reading the analogue port. measure the time between successive rising edges an take the reciprocal to get the frequency.