Thanks for the responses.
As I mentioned, just ignore the style. That's just how it was last saved. I never try to work with a model with anything but a bare-bones default style.
Earlier, I tried making a new document and pasting things in one at a time with new layers... this did not solve the issue.
I agree that there can be one or two modest simplifications to the pallet, and that that will reduce the number of points in my model overall, but that would be a performance boost rather than a help with my mysterious "ghost" objects that are pasted in with no lines or faces, only a bounding box. While there are perhaps a thousand copies of this shape, the shape itself is almost as optimized as it can be.
In a possibly related issue, I have been able to use the "Info" palette's drop-down menu to assign selected objects to a new layer. This is very handy and has helped my workflow. But although objects seem most of the time to follow instructions, turning on and off appropriately when I turn visibility on and off for the various layers they are assigned to, there is another issue. When I use the Layer palette's "Color by Layer" option, not all of the objects are correctly colored according to the layer they are actually on. For example, I have layers that seem to have multiple colors of objects on the same layer--some objects are "borrowing" colors from other layers. (There is no manually-applied color interfering.)
I'm uploading the file again for anyone who's interested.
Any further thoughts?
palette 2 d.zip