cylinder scoring after rebuild

Hello every one ,  a long time ago i built  1980 custom 1197 , Well the other day I bent an exhaust valve and cracked the guide not paying attention during degree in cams and changing a shim , my fault for not paying attention,  so i had to pull the head for the repair, I pulled the block to put a fresh base gasket and found cylinders and pistons  had some scoring so im probably going to re hone and buy another set of pistons unfortunately $$$, I had been using  foam filters on velocity stacks and later switched to APE pod filters none of which were ever oiled ( not the best decision ) , The machinist believes this is the cause , hard to say  MTC instructions were followed,  the block was processed at APE which do great work , the block was washed and bore brushed , I checked ring gap before installing top end and every thing was spot on . I am tempted to do a full tear down to install a 6speed transmission I had gotten a along time ago its been sitting in a box collecting dust , I had planned on doing this next winter , Not sure on that yet , are you guys coating piston skirts on assembly ? 

Pics of the bores?

I will post pics tomorrow , currently parts are at my local motorcycle machine shop .  I do believe score marks are top of the piston ring landings and lower skirts . dropped off today for bore measurement, all my equipment is currently in storage since moving so need outside help . Cheers