Without having the 3DM file, it's hard to see why Flow is not working out.
You could try this technique below. I've used it to place a raised strip of variable width chrome trim down the length of a car body.
1) Draw 5 curves to represent each extrusion of the lower-right gill.
2) Select the 5 curves.
3) Construct > Curve > Project > Select the top, front, or right projection as required.
4) Select the fish as the Projection Target.
5) Now your 5 curves are formed to the surface of the fish. These will be used as Rails for a Sweep. Make 10 appropriate sized closed curved profiles (one at each end of each curve for a taper) and Sweep each Rail.
6) Mirror the swept gill solid objects to the opposite side and Boolean Union the 10 strips to the fish.
A variation of this technique would be to project just a two curves (Rails) and design two closed curve profiles that include the ridges to make all 5 gills. Then perform a 2-Rail Sweep.
Something similar might work for the large gill behind the eye. I also think a Network might work to create the fish while integrating the large gill, all in one go. Would need to have your file to test.
Ed Ferguson
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