HI Ross @rfranks ,
That is indeed a problem: because the edge itself is not ‘flat’, you’ll have to move parts down and/or others up. Or cut the bottom away (Box trim in Orthgraphic Mode gives a pretty decent result, but it”s a bit like a Boolean).
What you might try, is to Select the bottom in Edit Mode (as good as you can) and then enable Proportional Editing and Scale the Bottom to zero in Z.
