Is there a way to setup an interrupt to trigger at n number of clock cycles from now?
Use a timer to count the system clock and preload the counter with an offset that overflows in the desired cycles.
Use a timer to count the system clock and set a compare match a desired number of cycles out.


To expand the number of cycles, you can do fancier processing in thee Isr but the basic gist IS the same.

Other approaches also exist but the two outlined here are easier.