Arduino with TCXO?

I do not comprehend how [ChipKit] implemented the software part

There is an arduino-like IDE for the ChipKits called "mpide" that implements most of the same functionality and libraries as the Arduino IDE (though it seems to be somewhat stuck at a version slightly earlier than the Arduino 1.0?)
http://chipkit.net/started/learn-basics/mpide-quick-start-guide/
micros() should work fine. I'm not sure about attachInterrupt() (and it might depend.) The exact nature of pin-driven interrupts tends to be subtly different between vendors.