heya got a little piccy to help me explain sorry for the lameness of it but it may help you here and there.
If you look on your ref and your model you'll notice the neck is very thin I suggest you scale it like shown by the red arrows on my pic.
I don't know what you mean by clipping (I am used to that term meaning hiding graphics or clipping views in 3d environments) anyhow,, It cud be you mean 'cutting' or welding.
The blue dots on my pic indicate the vertices,, if you look I am just guessing where most of them are but I'm sure you could weld a few of them and save up on some polygons (worry about this when you feel comfortable modelling).
The orange shaded by applies to the whole top of the model I'm suggesting you look into either keeping the whole model flat shaded or read up on some smoothing groups (again do this when your comfortable with what your doing).
But yea I think the main thing is just scale the neck properly, unless your trying to do something else?
Peace
Show