Motorcycle Repair: top end, light scratches, rod bearings

Question
QUESTION: HI Mike I have a 86 evo, top end started making noise so I did a top end job. Its now 5 over with weisco 10:1 pistons , but the rear cyl. still making noise, the rods had no up and down play ,but some side play checked with feeler gauge .014. Ive replaced lifters, push rods and rocker arms. Only thing I did not replace were the wrist pin bushing. I took the top end back off, I can feel slight movement in the pin when I wiggle it the bushing,rear cyl. is looser than front, so Im having them replaced. Now to my question, I also notice a few light scratches on both front and back pistons skirts and cyls. Could this be from the bushing or maybe a bad bore job any advice would be appreciated. Thanks

ANSWER: How many miles did you put on the motor before tearing it down again?
Mike

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QUESTION: HI mike I put 100 miles on before taking it apart to check wrist pin bushing and rod bearings, the noise sounds like its in the top and not the bottom,my concern is that my piston already are showing light scratches on the skirts, and if its not wrist pin bushing maybe the pistons are not fitting the cyl. right. Im having pin bushing put in and cyl. and pistons checked. Also when it was running I listen with a mech. stethoscope and the noise was loudest right between push rod tubes just below head gasket area I know its hard to say with out hearing it yourself but any advice would be appreciated Thanks Again.

Answer
I would have the cylinders checked to make sure they were honed correctly. Since you have a EVO motor you need to make sure the cylinders were honed  and checked with pressure plates on. If they mic out correctly then your pistons should be fine with light scratches. With 100 miles they have not even had time to break in. With the noise you are hearing, did you check the cam bearing?
Mike