Alright, i'll bite.
Using multiple layers doesn't suddenly make your drawing better. Using more layers means you have more room to test, fool around and experiment with different effects and shading to get your desired effect. This is If you are worried you'll mess up what you have already. If people can paint on a single canvas and work it to get an amazing image, you can do the same on a computer without the mess.
Anatomy should always be a concern, you can't skip the fundamentals and go straight to coloring. This was brought up as of note was to bring to light your question on why your skin was missing something. From what I can tell, to put it bluntly. Your coloring is flat, there is no depth. I get the impression of multiple light sources and it feels as though the skin was tightly wrapped around a board.
Well, scanning the original and doing line art isn't wrong. However, you should avoid doing "Hairy lines" or "Sketchy" ones, save that for your original scanned image and planning phase. The line art should be a clear outline for the image and displaying the sketchy lines without a style is very distracting.
A lot of good artist normally give you their own take on how the whole drawing / coloring process are. It's their own method and I can bet that most of them closely resembles afterenglish's general steps.
I am sure you've been told this a million times. Anatomy is one of the cornerstones of drawing, learning about it will obviously tie in with how coloring and shading works. Which in turn can help you with your problem now.
I'm sorry, but you mentioned three years of doing digital art self-taught? From what I can tell.. you absolutely qualify as a starter, and there is no shame on being one. Put your ego away and take a slice of humble pie. You won't ever improve if you are so defensive and won't take solid advice from others.
As someone once told me when I first started drawing myself and asked him about improving my coloring.
"It doesn't matter how well you can color if you can't draw and skip the basics."