you'll be better off by using a geosphere for the nacelle collector... it smooths better, uses less polygons, and it's easier to map.
orient it's positive Z forward.
also, don't "extrude" things from previous things... try modelling things separately and then weld their unions.
instead of "growing" as you go, try "clay-ing" in.... if you know what I mean
of course there's no "right" way to do things, and you might want to use the tool you're most confident with,.... but if you can get past that and forget the tools, and instead just focus on the procedure and tecnique, you'll nail it in no time.
you will notice that you sometimes get used to geometric proportions, measured structures and consistent volumes, and it might come a time where you just have to weld in that particular piece, and it either breaks your structure, or ruins the design.
solution: don't take the structures for granted.... just know the limitations of the tool and the mesh, and use them to work your way around the problem.