RE: Fairings at the wing root
OK, the green in the image below shows just what added side area the cowl is going to add to the existing airplane. Not a lot. All that other stuff that isn't green is already there and works as side area already.
It actually takes a fair amount of additional side area up front to have much affect. Why? Because the rudder/fin side area is usually about twice as far from the neutral point as the up front stuff. Leverage works everywhere there are levers.
I'd bet the farm the increased rudder is going to more than handle whatever effect the front adds to the situation. Truth is, from personal experience, I'd want a bit more increase back there just for the additional power. Especially since the model seems knife edge challenged. PLUS, the new outline just looks better than the original.
I don't remember, can that rudder snap that airplane with just elevator/rudder? Or do you need to hit the ailerons too? If the answer is that the ailerons are needed, then if I were you, I'd double the increase back there.
If that airplane wing is non-tapered, the wing planform is a rectangle, then I wouldn't even begin to worry that the increased rudder area could cause problems.