Sure I can help you with this but first try taking a look at this http://interface.khm.de/index.php/lab/experiments/arduino-frequency-counter-library/ this library will count frequencies of up to 8 Meg on a 16 meg 328 MCU assuming a 50% duty cycle
you can get your 1 meg out using a divider on the Xtal for the MCU.
Cheers Pete.