You're going in the wrong direction. You already have beautiful lines, and you're just going to leave them dead in a ditch somewhere to rot?
Get the lines to something more suitable for pixel art first....if you don't have Photoshop or the like, this can be pretty difficult unfortunately.
But essentially, get it as black and white as possible....the less grey the better.
Then, fill in everything with the basic color. Don't worry about lighting or shading or dithering or anything like that. Don't go overboard with the amount of colors. If you use more then about ten colors, I'd start to worry. Just be bold and messy, and cover all the white.
When everything is fleshed out, you can pick a light source and start to sculpt form with lights and dark.
From here, you can start to refine and polish. This is where you'd start to use more pixel-specific techniques like dithering and antialiasing.
That's just how I would attack this....it isn't an instructional rulebook, but rather just guidelines. And remember, post your progress and we'll help you along the way. ^_^ Hopefully this is helpful.
The main point is to not be worried about the details until you're much farther along.
Good luck.
I am he as you are he as you are me and we are all together.
