>I noticed that the original model does have several duplicate pieces stacked up on top of each other, 2 copies duplicated in one spot and 3 copies in some other spots. Is that possibly causing some confusion?

I have seen that and kill some of them ;)
But that was "the one surface" of half cylinder who pertub me :) (false reflex of the polys of sktechup :)
As Copy / Move lines selected is permitted no problem to use the lines :)