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The initial question was can After Effects make a composition that is an hour or more in length. The answer to that question is yes it can. This would allow you to create a non-looping animation. If you are trying to create a looping animation though you can also make a shorter, modular animation and stack it in your NLE as Grinner suggested.
I have never heard of anyone using animated GIF images in video projects. The GIF format was created specifically for web work and as such was purposely created to use a limited gamut of colors (256) which results in color banding and jagged edges. For still images the most common format is a TIFF (which supports millions of colors and an alpha channel for transparency) and for animation would be either an image sequence (again usually of TIFF files) or a video file that supports an Alpha Channel (such as an AVI or Quicktime file).