Don't get discouraged! It takes everyone a long time to get this down. It's also different for different people - how you abbreviate, how much you need to write down, etc.
Think of the diagram as merely an outline. Do NOT think of the diagram as "notes," the way you took notes in school. The outline is going to help you know where to go in the passage to get the information you need, but it is
not going to answer all of those pesky detailed questions for you.
You should be able to use the diagram by itself ONLY for the general purpose questions (eg, main idea). You should NOT be able to answer any detailed questions from the diagram. Instead, the diagram should help you decide (quickly) which paragraph is most likely to contain the information you need to answer the question. Then you have to go to that paragraph and dig in, looking for any keywords that were in the question, until you find the sentence or two that will be useful in answering that question. So a diagram lacking all those details shouldn't stress you out or make you feel lost, because you're going to use the passage itself for that stuff.
So go back to some of the previous diagrams you've done. Do they let you answer the "main idea / big picture" questions? Do they allow you to determine which paragraph to go to on the detailed questions? If not, then you're not recording the right information. If you can't do the former (main ideas), then you aren't noting the "big picture" info and you should take the time to do that (with SERIOUS abbreviations, though!). If you can't tell what paragraph to go to for detailed questions, then you're either not organizing the information well or you're not noting down the main idea of each paragraph. If you have a bunch of details written down that would allow you to start tackling a detailed question, then you've written too much down.
The other thing: in terms of abbreviations, they should be serious enough that, if you put this diagram aside for a few days, and then came back and looked at it without the passage, you wouldn't really know what it was talking about. Remember that, during the test, you're only going to be using the diagram for abotu 5-6 minutes. After that, you don't care about this info because you're done with it. So keep that in mind as you decide what is worth writing down and how you should write it down.
Here are some other sources for reading:
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http://magazine.uchicago.edu/ - particularly articles in the "Investigations" tab
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http://harvardmagazine.com/
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http://sciam.com/ (This can get a bit too casual for the GMAT, but it's worth including because of the science topics!)