It's common to have ever so slight scoring on the skirts. Excessive (that you can feel with your finger) scoring should be looked into as the aluminum will begin to "rub off" on the cylinder sleeve and eventually result in a siezed engine.
Running lean for a short period will not score a piston usually, there is excess oil in the crankcase for that purpose. What it will do is make any other problems MUCH worse. It raises the combustion temperature significantly so the aluminum is more likely to gouge if there is anything in there to cause it.
Very small dirt particles can cause slight scoring and steel particles from an uncleaned cylinder post-hone can also cause it. If you've already reassembled and leak checked, I'd say run it and just keep an ear out for anything unusual. If you hear nothing, ride it like you stole it.
