Update 3/10/2018 : Added the File Set 0.2 mm clearance.
Ac...cording to your comment, i remove the 0.5mm clearance set that is too loose
Depending with the accurate of your printer, you have other choice :
STL file set 0.1 mm clearance, 0.3 mm bevel 5cm cube size
For 0.1 file, the hole of the E piece is 10.2 mm ( 10mm +0.1mm + O.1mm)
and the unit cube is 10mm-0.1mm -0.1 mm = 9.8mm (see picture 3DBuilder measure)
If the hole it too tight for you , replace the E Piece with file = "E 5cm 0.1 Big Hole 10.5mm.stl"
-2 STL files 0.02 and 0.04 mm clearance 5cm hight 1mm bevel
Remember that if you inflate thean stl file, the clearance inflate too= more loose.
And if you shrink it the clearance decrease.=more tight