Marc, you are running into the situation many of us have run into: many AVR libraries used AVR specific techniques to squeeze capability & speed out of the platform and they do not translate well to the Due or other platforms.
The forum here has some posts that are very good for specific situations but no one has compiled a comprehensive "how-to" (maybe we've left that to our good friend Marc?)
Thanks for the update. I may have just created a solution... It's a simple counting-up app, from 000 to 999. (it goes into my blog, tomorrow) The next question I have is, how do I embed it into an interrupt?
Between 7-Segment displays, I'm using delayMicroseconds(4500). I'm using three 7-segment displays.