Spoiler: Big pic

Here is a pic with the instructions written out on Gimp layers. Begin reading at the bright green Instructions Layer. Or I have step by step instructions written out below.

*Note: Right Click on a layer or group to get the menu for "Alpha to Selection," "Merge Layer Group," and "Add Layer Mask."
*Note: A folder is called a "Group" in GIMP.
*Note: Gimp uses the word Duplicate for making copies then labels the duplicate as "Copy." Just take note of it, roll your eyes, and keep on working.

Step 1: More Prep
- From the "base" layer select "Alpha to Selection."
- On the Separated Layers group select "Add Layer Mask"
- On the Shading/HL group select "Add Layer Mask" (Remember the mode for this group needs to be "Pass through.")

*Note: I prefer having the mask on the whole group. This way, if I ever color outside of the lines (like I always do), it doesn't matter.
*Note: I usually "Delete Layer Mask" on any layer within the Shading/HL group. You don't have to do this since these layers won't actually be visible. It just looks cleaner to me and helps me keep things a bit more organized in my brain.

Your "Layers" dock should look something like this:

Step 2: Coloring
- Color pet by coloring the layers in the "Separated Layers" group. I like to do this with the "Shading/HL" group hidden.
- Once all coloring is finished, work your way through the remaining layers from bottom to top adjusting and adding things as you go.

Step 3: Making Colored Shading Layers
- Make the "Shading/HL" layer visible.
- Duplicate "Separated Layers" group.
- On the "Separated Layers copy" group:
-- "Merge Layer Group." Now it is just one layer.
-- "Delete Layer Mask"
-- Change "Mode" to "Multiply"
-- "Duplicate Layer" giving you a "Separated Layers copy #1" also.
*Note: I've renamed my shadow layers to "Shadow" and "Dark Shadow". So that is how I will refer to them.
-- Move "Separated Layers copy" under your "Shadow" Layer.
-- Move "Separated Layers copy #1" under "Dark Shadow" Layer.
-- Rename "Separated Layers copy" and "Separated Layers copy #1." I renamed mine "Shadow Colors" and "Dark Shadow Colors"
*Note: Your pet will all of the sudden be VERY dark. Don't panic. It means you are doing it correctly.

Your "Layers" dock should look something like this:

Step 4: Add Layer Masks
- From the "Shadow" layer select "Alpha to Selection."
- On the "Shadow Colors" layer select "Add Layer Mask"
- From the "Dark Shadow" layer select "Alpha to Selection."
- On the "Darks Shadow Colors" layer select "Add Layer Mask"
- Drop down Menu "Select" -> "None" This gets rid of the selection. So you aren't trapped making weird unintended coloring.
*See Looking better already!

Your "Layers" dock should look something like this:

Step 5: Adjusting Shading Colors
* This is where you decide the feel that you want for your pet. Bright and poppy, Dark and broody, or something in between!
*Note: Do this for both the "Shadow Colors" layer and the "Dark Shadow Colors" layer.
- Click on the colored image, NOT the mask you just applied.
*Note: I put a purple arrow pointing to one in the image below.
- Go to the "Color" drop down menu
- Select "Brightness-Contrast" menu
- play around with the levels until you get what you want.

Your "Layers" dock should look something like this:

Step 6: Making Colored Lines Layer
*Note: This will be very similar to what you just did with the shading layers.
*Note: Make sure the "Lines" layer isn't visible.
- Duplicate "Separated Layers" group.
- Duplicate "Shading/HL" group.
- Move the "Shading/HL copy" group into the "Separated Layers copy" group
- On the "Separated Layers copy" group:
-- "Merge Layer Group." Now it is just one layer with the shading included.
-- "Delete Layer Mask"
-- Change "Mode" to "Multiply"
-- Move "Separated Layers copy" under your "Lines" layer.
-- Rename "Separated Layers copy." I renamed mine "Line Colors"

Your "Layers" dock should look something like this:

You can be all done at this point if you want!
I like to go in and make some fine tuning adjustments on the "Line Colors" layer.
- Click on the colored image, NOT the mask you just applied. Just like earlier for the shading layers.
- Take a small brush and adjust the colors to make the lines blend better where needed.

I hope this makes sense and is helpful