I don't know anything specific about your bike, but in general you should get a service and repair manual, asap. This will tell you the acceptable side clearence of your rod ('arm'), along with everything else you need to know.
When you bring your cylinder in for honing, you might find that it needs one or two sizes bigger piston (The machinist will tell you), thus make sure you can trade your piston in for a bigger one, somehow.
If it was my engine that was run low on oil for any period of time, I would split the cases and inspect/renew the bearings, rather than having them fail regularly during the next couple of seasons.