After cutting out 4 pieces for the two protrusions, I used a process I call contour sanding to make them fit the shape of the hull so they have the same appearance as the photo, where they look like they are pushed into the sides of the hull.
This is done by adhering, or holding, a piece of sandpaper to the part of a master you want the new part to conform to. Then sand the new part until its shape matches that area it needs to fit to on the master.
You can see here where it's supposed to go, but the tip of my piece is flat, the side of the hull is angled and curved.
Sand. Sand. Sand until it fits.
I did the same with the back half.
I glued the two halves together, then to get an exact fit, I applied some mold release to the hull master where the parts will go. Then applied some fresh-mixed filler to the areas where it must fit against the hull and pushed it into place. This eliminates any gaps and is exact compared to just the sanding.