Help with settings

[OnCor 0]

Hi all. I am trying to incorporate a "window" in a box I've designed for some electronic components. This opening will house a little display. On the back side of the window are four raised areas that the display will screw down to. For some reason I'm getting bumps on the front side of the box that are caused when the raised areas are printed. The wall of the box is almost 2mm thick. The box prints top down, so the wall is printed vertically. What setting(s) is/are needed to help alleviate this protrusion of the inside elements through the outside shell?

 

For some reason the Y axis also got out of alignment on one side of the "window" as well. I had a support in there with 1.5mm of gap between the edges. Any thoughts on why the printer might have gotten out of alignment in that particular spot? The rest of the side panel seems to have printed just fine. Could this be a slicer issue?

 

Any help is greatly appreciated!