Hi Gary,
Do you have some Arduino code somewhere showing how to use it as a counter?
I am also wondering if you would be better off connecting an accurate clock (such as the 1pps on a GPS module or from an OXCO) then using interupts to gate the frequency input. I have built an Arduino based WSPR generator designed by W3PM some years ago and it is accurate to less than 1 part in 10Million.
Cheers,
Peter - VK2AN