Looking for guidance in frequency measurement

Thanks for that explanation. It appears that FreqMeasure Library, for Measuring Frequencies in the 0.1 to 1000 Hz range, or RPM Tachometer Applications would be best for my needs. Why do I lose pins 6, 7, 8 on my Mega in addition to the measuring pin 49? That seems pretty expensive?

Am I able to generate an output frequency on one pin and input to pin 49?