I did try to have a high frequency interupt which was a counter to generate another interupt at variable frequencies but this bogged down the Due too much.
I've started having a look at the SAM3X/A document and I've spotted something which might be useful. On page 882 Figure 37-10 WAVSEL=10 with trigger it shows the counter counting up to RC and then being reset, or being reset by a trigger. I think there is a compare which can be used for this trigger, but as you say it will take some diging!
My issue is relating to stepper motor drive. Adding the control to the main loop() function with delays isn't the best on timing and at worse if you use the delays method the Due bogs down and becomes only useful for one thing and moinitoring inputs (switches or serial), or presenting outputs (LEDs and TFT), give up.
Thanks for your help. If I get any further I will post back here...