In case this helps anyone else, I thought I'd throw this out on the Forums. I needed more precision than what micros() provides, since it only has 4us precision, so I wrote my own timer using Timer2. I chose Timer2 so that I could minimize impact on other Arduino functions, and I definitely didn't want to use Timer1 since it is what the Servo library uses, and I wanted to maintain functionality of the Servo library.
Here's a brief description of my code, and a link to where you can download it:
"I wrote a "libary" to get 0.5us precision on a "micros()" replacement function, so that I can get repeatable results reading a PWM or PPM signal, to within 1us. I searched all around the internet and could not find something comparable (or that was easy to use, and maintained the Arduino's ability to write PWM signals via the Servo Libary), so I think this is my first real contribution to the world of Arduino and Radio Control."
http://electricrcaircraftguy.blogspot.com/2014/02/Timer2Counter-more-precise-Arduino-micros-function.html