The pin just goes through the piston and conrod small end (oil first), then fit both cirlips. I've done a couple of full rebuilds on the ybr125 in the past year, and the xt (new type) is the same engine. Piston size is 54mm, not to be confused with the 57mm piston of the old xt (sr125).
Edit to add: get the scoring on the barrel sorted out first, don't be tempted to cut corners, it just costs more in the end (and leaves you standing at the side of the road, swearing at your bike).