Hate to say this, but if you can not take a functional board/EBI example and modify it - you are going to have troubles with anything.
The interface to the controller is going to be similar for any display it supports. If it does not support your display - there is nothing that will change that.
I think you were looking for help in the wrong place. I would have talked to the LCD manufacturer or the display controller manufacturer if there was any question of being able to function together.
I do wish you luck though!
[Edit]I saw no reason to just increase my post count so - If you want Atmel response - look for the Atmel people or use
at91support@atmel.com - this is a public forum with public responses. I know you are bitter, but just move on. Atmel was not the best solution for you.[/Edit]