Mike,
DA Rock made some important points about what you want to do and how to do it.

It took me 3 months to get the cowl I wanted just right for my 21 century cub design that I am working on. One of the biggest issues I had was getting the exhaust portion of the cooling system nailed down. It required coming up with a way to duct the hot air out of the engine compartment through the fuselage and venting it in a low pressure area without adding to the drag or frontal area of the aircraft. All told it was about six months for the whole system to be developed, I still have not finished up on the plane, as flying and other projects have cropped up. All told this plane has been three years in the making but the end result will be worth it.
As far as your question about the small intake I think that is due to the high speed, and the fact that they leave the head exposed. I am just guessing about that but it seems to be a logical explanation.
I would suggest that you read Andy Lennons' book on designing and building RC aircraft. He has an entire chapter devoted to cowls alone, if it was that important to him I would say it is an important design consideration to all of us. In it he mentions how the British Hurricane use the heat produced in cooling to add to the thrust of the aircraft. His setup for cowled engines are set up using the principals of a jet or rocket motor to use the heat produced as additional thrust. While in a model the added thrust may not be all that much but it does make sense to use everything you can to enhance performance.

I will see if I can scan that chapter in for you tomorrow night so you can read it.

Regards
Paul