I'd go back to Square One in Illustrator. There's nothing that says you can't create as many layers as you need in Illustrator, and move the appropriate paths and whatnot into those newly-created layers.
Make sure you give these new layers names. It helps a lot when you're in AE. Most Illustrator folks I know skip this step, much to their confusion later.
If your brand-new Illustrator document doesn't import properly as a comp, it's not you, it's AE Weirdness. I'd start by doing the easy stuff first: quitting all applications and starting them up again, restarting the machine if that failed, shutting down the machine if restarting failed... you get the idea.
And I know you didn't intend it to be so, but that youtube movie of yours darned near induced motion sickness in me. But you were in a hurry. I understand that.
To be honest I don't even know how to view the layers in AI, I have no expirence with the software, but you do point out a good point that the problem probably is AE, seeing as a PSD made from scratch can't be imported properly. I'll try restarting and doing some stuff see if it fixes it.
That was the obvious thing I was missing the eps was CYMK which was preserved from AI to PSD to AE, I just went into my PSD and changed Mode to RGP (without merging layers) and as you can tell by the video these are simple colors with no blending modes so I ended up not having to worry about tweaking it back to the orginal colors.
Thank you so much, I keep forgetting when something doesn't import somewhere (like images into a PSD) it usually comes down to color space.