All depends why reboring it, if the cylinder measures size you say then never been rebored. The cylinder on your year although called 56mm is actualy 55.95mm, if the cylinder is not damaged then just get it honed. If honing the cylinder then this piston is what you need.
https://www.ebay.co.uk/itm/Yamaha-DTR125-DT125-R-DTR-125-56-25mm-Bore-Namura-Piston-Kit/292513505226?hash=item441b29dfca:g:jyEAAOSwwbdWQwnA
Whatever size piston you buy whoever is reboring it will bore and hone to match what piston you supply. The best reboring is done by Karl at KPM as had them do a
few and also by PJME. Karl charges £30 for a bore and hone with return postage at £10-16 postage depending on courier and insurance required.
He will also fully port your cylinder for £100, just have to tell him what your after like more midrange etc or more mid and topend like a YZ.
http://www.kpmotosolutions.com/