Yeah, the basic concept behind animating is that you use bones rather than geometry. Thus the position of the vertices in relation to the bones is how the model will animate. Basically if you were to use the animations of the spycicle, you'd need your model to be as close as possible position/size-wise in order for your model to animate properly.

So yeah, importing a decompiled weapon will do two things for you:
1) It will give you the necessary bones that you'll need to attach your own model to
2) It will give you a good idea of where to position your model

So once your done modeling your own weapon, you'll want to just position it correctly and then delete the spycicle.

Does my old method of compiling not work? Use GUIstudioMDL + the sourceSDK to compile. It's a complicated process, but I explain it in my original video.

Oh yes. Definitely. I thought you were going to try to use the old one for everything. The old one describes the modeling process in much greater detail. When it comes time to compile, use the new one.

Without doubt, a lot of that material is outdated. You can definitely check out my new tutorial though.

I'm not 100% sure what could be wrong. I don't use the latest versions myself. Try contacting the author of the SMD tools script: http://steamcommunity.com/groups/BlenderSourceTools

Oh that image just describes how to paint things realistically. The example he gave was 1 object overlapping the top object. So you can't have a paint stroke going over the top one. That wouldn't make sense. I wouldn't worry about it too much.

Just paint things like they would exist in reality. Don't do anything that couldn't exist.

When you import the .dmx or .smd file, make sure to uncheck the box that says "Append existing model" (bottom left of the import screen). Otherwise if there are ANY bones in your current scene, you won't get a new rig.

You can't have 2-sided faces. You can only see the texture from one side of a face. That means you can't have "open" models.

You should seriously get a real mouse. Otherwise I'm fairly certain you can change middle mouse button to another key: User Preferences window > View & Controls tab > change the key.

Assuming you have a mouse with a midde mouse button:

Middle Mouse Button - rotate
shift + MMB - pan
scroll wheel - zoom