Hi Chipp,

re:
> That said, I didn't understand how you were able to 'flatten' the control points? Can you
> elaborate? It sounds like a helpful skill to have. Thanks!

That was by surface control point editing. First select the top face and use Edit > Separate to break it off into an individual surface object.

Then I used Edit > Show pts to turn on control points, and selected the middle set of points about like this:



Then go to an elevation view like the Back or Right viewports, and use the edit frame to flatten the points using "flat snap". That's where you grab the corner sizing grip and drag it downwards until you see the "flat" snap point engage, like in this example here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=3378.4

If you don't get any flat snap it means the thing was already flat, that's a way to test for planarity. Also it can sometimes be of diagnostic use to do the opposite and drag the corner sizing grip outwards to stretch it and amplify the wiggles to get a better idea where they are.

Hope that helps!

- Michael