Do you really need to use an interrupt in this case? Is the microcontroller busy doing something else?

Couldnt you just keep checking the port pin till it senses a high, or low? Then start your timer and turn on output or turn on output first before starting the timer.

Then you could keep checking overflow bit, then you can turn off output and loop back to beginning.

If the micro is busy then an interrupt is the right choice.
In which case this all the above can be done in the interrupt routine.

I am in no way an expert on this and I hope others will correct my way of thinking but it makes sense to me.

Regards

James Krushlucki