I'm interested in building a King Cobra (SIG), I want to
modify it to use Flaps. My concern is that I will give up some
aileron surface for the flaps. Is that a problem? Also I want to
use a FX 91 engine rather than the recommended 60. Will there be enough prop clearance? Is a 91 to much power? Here
are some other modifications I'm considering.

1. Use external servo mounting for the Elevator and Rudder.
2. Use micro servos one for each aileiron.
3. Use Retractable Landing Gear.

I would also be interested I hearing what the plane is like to fly.

Adding flaps won't take away any noticable aileron control. Roughly 95% 0f the aileron's effectiveness is in the outter half of the wing. Cut each flap about 6" long and control them from the aileron torque rods, then, add a servo to each wing for the ailerons. You'll love it.