Have you had a look at the code for reading from an RC Receiver on my blog ? it uses interrupts and the micros function to measure the time between pulses. In my Child Mode project I use this together with the servo library to put the Arduino between my Receiver and electronic speed controller. While you may be aiming for a different outcome, the nature of the project - read RC Receiver, do something with the signal, then output a servo/ESC signal from Arduino - would appear to be the same.
I like this approach because there is only one Timer1 and to my mind its better used to drive servos than to measure an inherently noisy signal. The micros function will give you accuracy in the region of 4ms, but in my test the original signal can vary by as much as 40ms from one pulse to the next, so using the 16 bit timer1 to get increased accuracy in the measurement is to my mind, not the best use of the available resources.
Now some good news -
Reading through the Servo library and some of the other Arduino header files, I have come across F_CPU, my guess is that if you investigate this, it may turn out to be a system wide definition of the CPU frequency. You will hopefully find that all well written libraries use this or functions that reference it in which case you can make a single change to have your Arduino adjust all/most/many of its functions to the new frequency. Without having investigated it fully my guess is that micros will include a reference to F_CPU and so my approach to measuring RC Input and generating the output should be portable between clock speeds.
You can find some code to test at different clock speeds here, but remember to adjust F_CPU first -
EDIT : F_CPU is defined in the make file, not an include file.