Hey stop motion is hard, I know, and this was pretty long, so you must have spent a buttload of time on this. Did you have your camera on a tripod? Remember light source, and how different lighting will effect dirreernt colors. I saw in the beginning when they were shooting, that the light flickered. I dont know if that was intentional or not, but it did add a little something. Tungsten lights make things more blue. Fluroscent makes things look more yellow. Use this to your advantage!
Also large areas of color, like green, will often give the rest of the shot a greenish look if you're not careful. If you're using a high quality camera, be sure to check your settings and ISO. If you have a crappy consumer camera, then I guess more power to you.
I didnt really like this, but I admire your dedication. Keep it up friend!