Fastest way to count pulses - Programming - Arduino Forum
It looks like timer 1 can be driven (clocked) by pin T1 just by changing the Clock Select. Its implied by Figure 17-1 that timer 2 can also be driven by a pin but I cant find how to enable it. I suspect you can replace the trigger in your code with the "Input Capture" part of timer 1 and have nearly the entire solution in hardware.
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