Look into projection unwrapping. You can project complex parts as uvs and unwrap the other parts via seams. Also: try to put the seams in places that normally aren't seen by the player (inside other geometry, in the back, etc.).

I don't personally use Gimp, so I don't really know what could be wrong. I did a quick google search that perhaps might help you: http://www.youtube.com/watch?v=ukuc256YjCs

Oh. Well that's not too bad. I'm assuming you use photoshop (if not, whatever program you use should be similar):

In photoshop you should see a panel in the bottom right labeled "channels".[dl.dropboxusercontent.com] If you don't see it, go to window > channels. From here you can edit individual channels of each mask.

Channel 1 = Red
Channel 2 = Green
Channel 3 = Blue
Channel 4 = Alpha (transparency)

Normally channels are used to control the amounts of RGB in each part of the image (with the last channel being reserved for alpha transparency), but the source engine can read these channels to be masks based on how much portions are colored white (white = full power, black = no power, grey = in-between). You can edit these channels the same way you edit anything else in photoshop.

There aren't really any tutorials to look at other than what valve provided. The pdf literally explains exactly what each channel does in terms of shading and lighting. My advice would be to re-read it and learn what each channel actually does. Looks good, though.

Wow, that's really odd. I'm almost certain part of your mask textures are not being used properly. Try mimicking an existing juggernaut sword (dig through some of the game vmt files to see how valve set the channels up).

Can you show me? I can't really do much other than offer advice on what I think is wrong.

Make sure you don't have the self-illum layer in mask 1 (channel 4) white. If it's white, your whole model will be bright. You might also need to adjust some specular highlight channels.

If the item you are making doesn't replace a slot that Valve designates, it won't work. I suggest making an item for witchdoctor in an item slot designated by Valve so you won't run into this error. Of course Valve might have made a mistake as they somtimes do, but I haven't checked out witchdoctor's assets yet, so I can't be sure.

I'm sorry, I don't really understand what you're trying to say. I suggest looking at an existing item to see how the bones are applied.

A model can be assigned to multiple bones, and in fact most do. You'll need to look into weight-painting mode (google it) to efficiently rig your model. I would suggest looking at the default item you are looking to replace and see how the bone weights are set up. Then mimic the setup with your own model.