You appear to contradict yourself... first you say...

...there is not enough time to sit and wait for the period to pass, lots of other tasks must continue while this pin is high...
then you say...
The period the pin is high varies a lot, so I can't try to run other pieces of code by 'squeezing them in'
Now you either want to run other pieces of code whilst your pulse is being generated, or you don't...

Either way, whilst PULSEOUT is running you can't do anything else in your code during that time. Chose a different method to generate your pulses (example HPWM) if you wish to execute code simultaneously with your pulse generation.