Hi Skyground, for your issue #1 removing those edges, it tends to be a lot easier to get rid of those earlier on in your modeling process rather than after a lot of stuff has been done. You basically need to use the Rebuild command (http://moi3d.com/3.0/docs/moi_command_reference10.htm#rebuild) on a multi-segmented curve to make its segments fuse together, then when you construct a solid or do a cut with that fused curve it will only generate one face rather than one face for each curve segment.

In an already constructed model it's more difficult to remove it, in your case here you'd need to delete the faces, select the 2 bottom edges of that area, join those together to make a segmented curve, run rebuild on the segmented curve to fuse it into a single segment, extrude that single segment to make a single face, trim the face to the surrounding edges, and then join it into place. I've attached a file where I've done that.

- Michael