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Khagalat - have you run a custom gearing strategy on AMR yet? That will give you gear results tailored totally to your character. If you haven't yet, here is a guide (but pick 'gearing strategy' for the sim type instead of 'beta v2' like the picture shows).
http://i.imgur.com/wBitmQb.jpg
I can also run it for you if you give me your character name and realm.
Lastly, as for simming things, we spend a lot of time make sure it is as accurate as possible. One of our recent set of tests shows that our sims match top players (indicating that spells and rotations are correct and reflecting what top players can do in game):
http://blog.askmrrobot.com/simulations-match-real-logs