If you program a timer to produce a square or rectangular wave, it will do so very, very accurately and continuously, without any jitter, and without any further intervention by the CPU. Get that working, using the simplest possible code, before moving on. Plenty of tutorials on that, plus study the timer section of the CPU data sheet.
You don't need to use interrupts to do that.
So far, your description of some sort of modulation of the signal produced by the timer seems to be entirely theoretical. Please explain, and post circuit diagrams and timing diagrams showing your intent.
But why worry about measuring something, until that something actually exists?