I believe that maxy is spot on. All of these sims have the same database. It is clearly very easy to set up a simulator in the climb out of Boston for a crew to practise taking over the aircraft and flying it in to the World Trade Center - especially if the visual of Manhatten is in the database.
How many hours would it take to perfect this aswell as the operation of the autpilot and taking out the autopilot to fly it manually at the final stage? I reckon with Bin Laden's financial backing they could have spent as many hours as they needed in a sim.
However no simulator company would hire out their sim without knowing that there was a qualified instructor in charge of the sim detail. Therefore there has to be some airline involvement - possibly Iraq Air?
All of the aircraft were 757 / 767 which is a common rating. Check the useage of 757 / 767 sims over the last two years around the world and you will find something out.