I'm trying to make a custom Companion Cube sign for the beginning test chamber sign, and I open it, the image isn't shaded in all the way, and when I do shade it in, the anti-aliasing is all messed up. Any help?

Try making the shading semi-transparent.

There's no shading on the direct file.

It's the side blurring I'm talking about.

If you have photoshop, use the blur tool.