Increasing the configured diagonal rod length in the firmware will reduce the amount of carriage movement, and hence reduce the print size on the XY plane. But first, check that you have your tower steps/mm configured correctly, by checking that your prints are the correct height.
Unless you have an error in your build, such as the pairs of parallel rods not being quite parallel, then you should be able to use the value you measure and it should give accurate prints.
Btw questions like this are better posted on the Delta Machines section of this forum.
Edited 2 time(s). Last edit at 09/09/2015 03:29PM by dc42.
Large delta printer [miscsolutions.wordpress.com], E3D tool changer, Robotdigg SCARA printer, Crane Quad and Ormerod
Disclosure: I design Duet electronics and work on RepRapFirmware, [duet3d.com].