I filed and sanded the hole in the fuselage skin to match the doubler, then match drilled. Unfortunately, I fouled up the first doubler cutting the dimples, so I remade the part and sanded it to match the skin, then dimpled, alodined, primed the mating surfaces and riveted in place.
Then I trimmed off the original flange from the duct and reset it in place over the doubler. I formed a new thin flange from epoxy and Aerosil as a base for more layers of carbon fibre. When they set I'll be able to trim the duct to match the outline of the doubler and start smoothing out the inner duct to exactly match the hole in the skin.