I've encoutered a weird thing happenging using the non-manifold add to join my brackets (actually only 1 bracket) together to the rest my structure.
Although I keep the tolerance small (10E-6) trying to delete, remake surface etc. the command seems to want to merge two nodes/points which destroys the model geometry. I've tried deleteing, redoing, copying cleanup, deleteing nodes, I think everything, but I cannot get it to work. Each time I want to join this bracket to the strucutre the geometry goes wrong. Is there something I do not understand?
Please see before and after shots below:
I'm seeing some extra surfaces that aren't in the before and after picture you posted so I'm not quite sure which surfaces you are trying to nonmanifold add.
If you delete the mesh and maybe also irrelevant geometry - and save it out as a test model - then you should be able to get the file size down from one gig and upload that instead. Others will then be more inclined to have a look at it for you.