I think that's the correct way to go. I assume you are using an UNO? Let timer 1 do the job when your trigger fires. In the trigger ISR you set the inital values for timer 1 ( the delay time until your pulse. The rest is done in a timer ISR. First for your initial pulse length, and than you create the pulses with OCR1 and count them in the timer ISR. After the last pulse you switch off everything.
I think you have to study the datasheet of the mega328 a little bit 