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My 2 cents:
Are those dimples? I would think that if combustion chamber and coolant & oil ports are fully sealed with head gasket (both has to be completely flat), the rest won't matter. Dimples are fine as long as it isn't close to any passages where it can cause leaks.
Make sure you account for decking when picking your pistons and rods. Also, if head was milled, check your valve / piston clearances. You'll probably need to degree your cams since any decking or milling will retard your cam timing. Adjustable cam gears will make life easy.
Need better pics of the surface. It looks like what you're seeing is where the surface will normally get some pitting because that's where the water is, and it doesn't effect sealing.
The only thing you need to change to account for decking the block is head gasket thickness, or if you're ordering custom pistons you can also account for it in pin height. Rod length is not how you account for it. And most people don't order custom pistons, so we're back to the head gasket. Degreeing cams generally isn't necessary if you get the right head gasket.