I am pretty sure the model is flawed. This resulted in the pieces not forming a cube.
I printed this out at .2mm resolution with default settings for Prusa mk2 (20% infill). I should have checked the dimensions in my slic3r because they seem to be scaled down in the z direction. Maybe I can just scale them back up so that the x, y, and z directions all have the same lengths? Or maybe I can just recreate your steps with some 3D modeling software.
Don't print this out unless you scale it correctly with your slicing program