Ok, spent the day trawling through the docs and internet yesterday and figured out a few things, but alas nothing that is a perfect solution.
I will have a look at the PWM channels at some point but that would require a re-wire of my connections to the shield. Not out of the question but I'm hoping to avoid that. To be fair the standard wiring for the motor shield isn't ideal any way as it's using the LED pin to control the direction of the current - loosing me a simple debug tool of flash if I've got a problem!
The Software Trigger is a little help, isn't ideal. My understanding of if it is that you can use it to raise an interupt from the main code that resets the timer. This might improve my last efforts a little as the code that is changing the motor phases and pwm will be high priority, rather than standard script...