Borrow a stethescope, or put a long screwdriver handle against your ear, you can narrow down where the sound is the loudest. Its really hard to tell anything without hearing it up close and personal..
In the late 70's I slapped rebuild kits into chevys and got away with a LOT of things I consider heresy today.. A bore being slightly off center is common but usually doesnt affect a street motor. I could rant a bit on your machinist... but,, again, without being up close and personal I dont know the circumstances/situation...