Thomas and all,
I ended up using two flex wires running through tubes, one on each side of the cowl that drive the cowl flaps and even though is not continuous due to the cylinder head, it still works.
When I started, I had the same concern and I built a flex torque cable driving small arms for each cowl flap, but it did not work well. The torque cable was made out of speedometer cable with the arms silver soldered, but it became pretty stiff and did not turn well.
https://www.facebook.com/fly.fliteskin shows a shot video of the cowl flaps
JG