I think that your original problem and perhaps this one is due to the way that you built the pylon. I'm unfamiliar with TC Mac versions, I'm using a windows version of it (long story), but does yours have verify menu? I used verify|check object, and it told me that ACIS object 11102 has a zero-area surface somewhere. When I passed a cut section through the middle of the nacelle, it revealed that the surfaces of the top of the pylon are within the nacelle, ie nacelle and pylon aren't a homogeneous solid. I investigated further and exported the pylon as .stp, when the .stp was reimported, it returned as two objects, the pylon and the nacelle had separated. The top of the pylon has a self-intersecting surface and its outer edges are what I would consider too close to coincident to the nacelle's skin. I started trimming the top of the pylon, and that led to the skin on one side of the pylon rippling madly....
So....converted to surfaces and untrimmed the pylon. The pylon surface is not sound. There are gaps in the skin, it won't heal or thicken. I think that you ought to rebuild the pylon cutting back the surfaces within the nacelle, and try to avoid coincident geometry, like the front flat surface of the nacelle and pylon. If you want to shell the pylon or provide cable routing, it's a good idea to do that before you start adding details, bosses, holes etc, they complicate those operations. Make pieces overlap when you add them, and trim them back afterwards with sacrificial objects. Overlaps and trims in solid booleans give more integrity and reliability in my experience, and you'll have a better chance of being able to shell the pylon or subtract a cable route through it. I'd add the cross piece and subtract the mounting holes from cross piece and nacelle as one operation to avoid problems from coincident faces, too.
Rebuilding the pylon will eliminate your dramas, IMO.
*edit* I passed cut sections through the pylon and checked the curvature of the profiles, and it's mostly asymmetric.