a burring hone is used to put cross hatching in the cylinder walls. this is to help the rings seat. Chic was right on the end gap for the rings. when inserting them in the cylinders to measure you'll need to set them just below the top of the cylinder, below where the carbon built up, that is the combustion chamber betwixt the head
and piston and then again at the bottom of the stroke, the point that the piston goes at the bottom of the cylinder. I believe it has about a 3 inch stroke. you'll usually find the gap wider there. if it is more than 4 to 5 thousandths you'll need to re bore or put new sleeves in. i'm not sure if the 2 gm has sleeves. most of the older Yanmars I've worked on did. The number on the piston is to show what orientation the piston is to be set in. the manual will tell you what side it goes on. if you remember what side it came from put it back the same. Like wise with the connecting rods, a number at the big end. if you don't remember, get a manual, as you could be running into some serious trouble.
when assembled, to break in the new parts
run the engine
for 30 or 40 minutes, at idle, till it is fully wormed up and then let it cool and retork the head
bolts. Then crank it up and worm it up again then get under way. give yourself a few hours to do this. run it at low rpms (1000) for at least 15 min.s and then bring it up to around 1500 for a few minutes then back down to 1000. do this a couple times then go to WOT for 3 to 5 minutes. then your good to go.