Pick a codec that renders quickly like GoPro Cineform or choose to render an image sequence. Make sure you are not using an unnecessarily high frame rate. Depending on the motion in your frame you may be able to successfully cut the frame rate in half. Loony Toons, in fact, most hand-drawn cartoons are 12 frames per second with every frame repeated twice so they can be played back at 24.
Unless the project is one continuous shot that is one hour long with no possibility of cutting it up you can break it up. I almost never string more than two shots together in one comp. Most of my comps are seven seconds or less because I work mostly on movies, corporate videos, commercials, and it's all live-action. The average time between shots in modern productions is around 4 seconds.
If I had a project like this, I would make the comps as short as possible, and as soon as I had a few seconds successfully designed I would start rendering. If the render takes longer than a few seconds a frame I almost always render image sequences because you never have to re-render the whole thing to fix 20 frames the client doesn't like in the middle of the comp.
If you are being paid for this work then invest in a background rendering option like RenderGarden. I have several and it is my favorite. On my main system render times drop by about 75%. A comp that takes 20 minutes to render using the Render Queue might take 30 minutes to render in the Media Encoder. That same sequence will render in five or six minutes with a good 3rd party background rendering option. Any comp I have that takes longer than a few seconds a frame to render is always sent to a background renderer.
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