I'm with Rusty
-I suppose the marks could be the one place in the entire cylinder that did not oxidize during the open period.I suppose it could be a watermark from trapped coolant.I suppose a lot of things, but;
-If the marks are below the top inch,and you can't catch a fingernail in them, and you have cast rings,I would ignore them. Forget about them.Pretend I never saw them.
-If you have chrome rings...Well you're in trouble anyway, so just fugedabowdit.
-If you have moly-faced rings;and the engine is on a stand, I might polish the affected areas with a bit of steel wool or Scotchbrite. Unfortunately this would then require careful cleaning.But if the engine is still in the car,and you can't catch a nail I think I would, try, to ignore the marks.
Since you've taken the pistons out, I would recommend to clean the ring lands out. If the marks are from anti-freeze, it will have gotten into there and may be gumming them up.But Ima betting you already took care of that.
I have done lots of heads-off work, where the cylinders got these marks, even with careful cleaning prior to the vehicle being pushed into the corner to be finished the following week. They all survived without smoking or compression issues.
I suppose one might ask, why try to save this little bit of coin on a build of this caliber? Yeah, it's hard to argue with that.....But I have a feeling your heads will be off again soon....
heehee