ORIGINAL: iron eagel
The cowl arrangement will add approximately 16 inches in side area to the fuselage, most of which is ahead of the stock COG. While I am fairly sure this will make the KE performance much better I am concerned this may affect spiral stability. Although adding more rudder area should negate this (I hope).
Don't sweat it. The improvement in aerodynamics is going to be well worth whatever MIGHT happen to the spiral stability. And if you do notice something, it's dead simple to add area to the rudder or fin. And it's easy to test the additions since you can simply tape card stock back there and fly.
Have you considered that the increase in side area should not include the side area of the engine. It was already there. So if you've figured the fuselage side area to be 16, then all that 16 sq.in. isn't actually additional.