Shifting a number right by n places is the same as dividing the value by 2 raised to the power of n.
Pin toggling, as proposed by 4iloand by myself in the third part of this answer, is ideal if you have an oscilloscope handy. However, it is incompatible with other uses of the timer PWM, Servo library Timer 1, which is discussed in the second part of this answer, is my favorite: it has single cycle resolution and low overhead.
This is also when you have to ask yourself what exactly you want to count.
However, for anything beyond a handful instructions, it quickly becomes tedious. Maximum measurable time: any method that does timing arithmetics on the Arduino is prone to overflows if measuring too long times.
On Arduino it is 16 bits, but in other environments it is 32 bits. The term word as used here refers to a bit value.
Solution Use the word h,l function to convert two bytes into a single Arduino integer. Shifting right two places becomes decimal 3.