Thanks guys, I really appreciate your help. I will try these things, i'm surprised to see rotating the model actually solved that problem. Printing vertical may not be too much of an issue, just slightly worried about strength of shaft because it can shear off easier than if it were printed horizontal, these are "RC Accessories" people use them in their Scale Remote Controlled Trucks so durability is an issue.
You can't use multiple meshes in S3D this way, you need to boolean those objects, if not model them as 1 from the start. Merge all outlines is a bit of a bandaid, but the results are inconsistent, and it often fills in cavities needlessly.
Look for boolean/merge options in whatever software you're using.