Update standard_parts.scad

Fixed: "TODO (from MCAD): proper screw cap values: instead of "height" will use METRIC_BOLT_CAP_HEIGHTS[size]+tolerance" this is not necessary because the cap height is the bold size so M3 cap is 3mm heigh.
Also fixed some tolerances because they where terrible big. On my print a M3 hole could fit a M4 bold and in the nut holder the nut could almost turn around. 
Removed radius from hole_for_screw and hole_for_nut to clean up the code and it fixed errors in the STL output of OpenSCAD.