Avoiding other issues...
There must be a slick way to turn interrupts on and off individually with minimal avr register writes.
Why do you have this "minimal avr register writes" desire? To turn off an INDIVIDUAL interrupt, you typically have to change a single bit setting in one register:
TIMSK1 &= ~(1<<OCIE1B); // Turn off timer interrupt
:
TIMSK1 |= (1<<OCIE1B); // Turn timer interrupt back on
Those should run about 3 Instructions each, and this isn't some multi-GHz chip where accessing an IO register might be unusually "expensive" because it stalls the pipeline and invalidates caches or something. If you want control of the individual interrupts, I don't think that you can get any "slicker." Now do you need to.
Note that you do NOT need to reinitialize the rest of the timer just to turn interrupts on and off, but that may mean that you will get an interrupt as soon as you re-enable it...