magnum 5.9 with aftermarket pistons

If you want clean, use ATF and a rag. But for measuring, they just need to be decently clean , not re-assembly clean.

Sure, you can just hone it. But it may or may not be any good. You gotta get some bore guages and check it for taper and roundness. If I saw bores that only had part of the hone pattern left, then I would assume some pretty significant wear has occured.

Can't specifically explain why the crosshatch is where it is, but block & heads warp in odd ways when torqued.