I file the big end, (rod and cap) .002" under minumum bore size top to bottom, and hone them until they're back round and to the right bore size.
It's worth noting that the common spring loaded type of cylinder/brake hone will do absolutely nothing to correct for an out of round condition. Even with the right equipment attempting to correct for out of round, bellmouthed, barrelled, tapered, or other wear/distortion patterns by means of honing requires specific tooling and procedures briefly described here:
http://www.sunnen.com/graphics/assets/documents/bd2da13109ab.pdf
