I’m using Slic3r with a RepRap Prusa i2. I calibrated the extrusion measuring the actual filament intake per mm extruded. I get the ratio of around 0.92. After this calibration the single-wall calibration objects are too thick. If I adjust by the single wall thickness, I get a ratio of 0.78 or so. WIth 0.78 I seem to get under-extrusion, gaps, etc., but with 0.92 I get all perimeters around 0.3 mm or so thicker than they should be. The holes are too tight, the outer dimensions are too large. In order to get a precision part I have to subtract 0.3 from outer diameters and add 0.3 to inner diameters. What am I doing wrong?
I’m using a 0.5 mm nozzle, 0.3 mm layer height, extrusion width set to 220%. Filament diameter measured with a mic.
I wonder - what was the end of this issue of yours? I am struggling with something weird of the same kind - printed a test of circle and bolt head groove - inner circle is of the right size, outer circle is larger by 0.35 while in the inner hexagon of the bolt head the distance between facing sides is 0.5 too large… Sounds like your kind of issue -can’t make model larger or smaller to make all three dimensions fit 
Still unresolved. I stopped paying too much attention to calibration and just tweak the extrusion multiplier so the prints look good. I suspect it’s a bug/feature in Slic3r.
Do you mean a hexagonal trap for the bolt head? Try heating the bolt in boiling water and forcing it in.
That’s the one - it’s actually a part of the traditional pair of extruder gears that I took in order to run tests of geometry before I start printing the whole thing. And the bolt head actually turns inside this trap while the inner bolt hole is of the exact size, and the outer diameter of the whole thing is slightly (0.35) larger than the design.