We went through the same thing. We upgraded to 4.7 and needed to take advantage of the profile generator. I don't know how big your system is, but our project took a couple of years, primarily because we couldn't get committed resources on the team. People could only devote a few hours a week to the project.
Like the other poster said, I think its important to have the business define the roles. For instance, shipping clerks and receiving clerks. Someone who knows what a "shipping clerk" really does down on the dock needs to list all of the transactions they perform. Then someone technical will take those transaction codes and the appropriate organizational values and build roles.
We had the best success when the business was able to devote the right resources to the project. We also had our audit team involved to make sure our work would be compatible with sarbanes oxley requirements.
It was a long and arduous process, but we have very clean roles now with little duplication.
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