I’m afraid I don’t have too much time to really get into this one.
But, I think what’s close to the root of the problem here can be wrapped up into a lesson on basic tidiness while modeling.
Try turning ON the setting for >View >Hidden Geometry. . . and take a look at all the extraneous edges laying around throughout the modeling space.
Secondly, I think this a good example for why it’s always a nice idea to group your geometry together at strategic moments during the modeling session. You get to decide for yourself, and your own work flow when these moments should happen. . . But I think in this case there’s a good reason to have created groups for your core model prior to all the gymnastics that you’ve run it through.
In doing so, there’s just a lot less chance of leaving element of the model behind.
My guess is that incomplete selection of the ‘entire’ model, prior to copy/pasting… and moving/rotating, caused the otherwise flat planes to be pulled out of their pristine state. . . hence the subtle triangulation which you’re seeing.
It’s a nice shape, and I think overall you’ve done a good job with it all. But, a little more attention to process, before going into all of the advanced modeling rotations will serve you well.
Getting back to your original shape could possible happen with the undo history, but after too many saves those options get lost, unfortunately.
I’ll come back and fine tune my comments tomorrow, I have a few things I’d like to also mention, as potential tips. unfortunately, for now, I have to try and force at least a couple of hours of sleep upon myself.