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So you have a few different things highlighted which makes it difficult to determine what you mean by flat and aligned. At this point you are trying to do 2 main things. First, when you set the rib web on a flat table with it slightly weighted down the web should be fully against the table and the flanges should be at a 90 degree angle to the web. Second, if the web won?t sit flat then flute the flanges until it does, which should need doing on most flanges. If the flanges don?t sit 90 degrees perpendicular to the web then bend the flanges until they do, which may need to occur on some flanges.
The web will always need a little pressure to align all the flanges, but after fluting you should be able to see down the line of holes on the flange with just a little alignment of the forward and aft flange. The small tab with 2 holes will be clecoed into the spar so don?t worry too much about that.
I think that should provide some help, but if not please try to post a picture of your issue or narrow down which step.