I have these sweet sniper rifle v_models that someone else made. The problem is there were no W or P models included. I am trying to make the W & P models myself. If there is a tutorial somewhere please point me to it.
Anyway, I've used Milkshape and got the rifle on the ground, no skeleton or anything in the views. I've assigned the textures and everything looks great for the W model. I'm not sure what to do from here. I try to extract a Halflife reference.smd and I'm getting an error - "Found vertex with invalid bone assignment". I'm not even sure if I'm supposed to do this next anyway.
So I've got the .ms3d file of the gun laying on the ground, what next?

Any help would be greatly appreciated.

Take the w_model of the weapon you were gonna replace, decompile it, import it into Milkshape3d, then import your custom model. Place it in place of the old w_model, then delete the old w_model. Go to the joints tab, select the only joint there, select all vertices of the remaining model, and finally click on Assign. Then export as reference smd and replace the old w_model's ref smd. Then compile the .qc.