Hey Jim! I would take your cylinder in to a machine shop and have them measure it. Just because it looks good doesn't mean it's in spec.
Maybe I'm just weird about things like this but I would replace all the bearings in your bottom end. The last two XR600s I built got all new bearings, new connecting rod, overbored piston etc. I guess I just feel since your in that far, might as well put new stuff in so you won't ever (hopefully) have to worry about anything going south.
The original engine from my '84 XL600 had about 22,000 miles on it when it lost a mainshaft bearing. Not real common but it happens. How many miles on your engine?