Ok so atlas loot fu has nothing to do with being able to see the items. Fubar data mods are just plugins to allow quick access to data. If you have the atlas loot fubar mod but no atlas loot it will not work. In the same way that if you have atlas loot but no fubar mod then you cannot hope to display the info in the fubar panel.
With that being said. Your stated question is actually 3 questions in 1 and actually provides us with no relevant information as to your problem. So saying " I'm only restating what I've already posted" will not work in this situation.
Now lets break down your question
For the first time since Cataclysm launched, I decided to update my addons. Once in game, clicking on the atlas loot button only brings up what would appear if I was accessing drops in atlas. I am unable to bring up a window where I can choose to view loot that is crafted, PVP rewards, etc.
I realized that atlas loot fu is not in my addons folder. Nor is it within any avilable atlas loot downloads. When I tried using my old atlas loot fu, the game disregarded it and instructed me to remove it as it was no longer in use.
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As stated above you do not need atlas loot fu to use atlas loot.
And for the TLDR version
In game type
/al
This should bring up the atlas loot window, if it is still blank then delete all the refrences to atlas loot from your addon folder and delete the saved var's and re download it all.
And in the future please remember that we answer questions based on what you ask, if you ask the wrong questions and or do not give full accurate information we will never be able to help you.
Happy New Year!!