One problem I am having here is that I have no sense of your level of competence with programming and with microprocessors. What you said in your Original Post "I have ZERO programming experience" is hard to believe. For all I know you know more about this stuff than I do,
On the other hand, if you really are new to programming and microprocessors I reckon you are starting with code that is far too complicated for a beginner because you are likely to be missing the experience to debug your code.
...R
Oh there is no doubt that I am using a lot of techniques here that are beyond my experience level to debug, but another problem with inexperience is that I do not see any alternatives to asynchronously generate pulses at microsecond intervals, vary the timing of those pulses at runtime, and do so with any other methods besides using direct port manipulation to save processing power and multiple timers with compare match interrupts so that I can bang values into the registers for those timers to quickly adjust the timing on the fly and turn on/off interrupt flags.
If there is an approach that I am not considering and don't know about, I certainly want to learn it.
Maybe PWM? Would it be possible to throw some numbers in a timer's registers to get a PWM frequency of my choosing, then also have a compare match interrupt that would simply increment a variable, and then at a certain value I could flip the PWM output pin to input to shut it off?
I am just really confused by how the timers work in general. It doesn't look like I can generate PWM and use CTC mode.