Printing circular holes that are correct in size is problematic for RepRap-based printers. There are a number of issues that can affect the printing of holes with diameters of 2 mm and smaller. One issue involves how the material is laid down while moving in an arc. When a nozzle extrudes while making a circle, more material is deposited on the inside of the circle than on the outside. This is because the inner perimeter of the circle has a slightly shorter radius than the outer perimeter. The difference in the radius size is determined by the width of the extruded line.
Skeinforge has a means to compensate for this problem by activating a plugin called Stretch. It's not a perfect solution, but it provides better results.
There's a handy hole calibration model that we'll need, and it can be downloaded from Thingiverse. You can find it at http://www.thingiverse.com/thing:28562. An assortment of M2, M3, M4, and M5 screws will be helpful in testing the...