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I had my cylinder heads off for valve tuning for a prolonged time period so moisture got in and some very mild surface rust collected inside the cylinders whose pistons were not in TDC (4 out of 6). Is this serious damage, will it keep corroding more, and is there a way to clean it?

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    I would try cleaning it with some wire wool with a little oil. Rub around the circumference rather than up and down the cylinder. I wouldn't use wet and dry paper since you want to make sure that there is no tiny abrasive particles left in the cylinder. Clean it well afterward with a cloth.
    – HandyHowie
    Commented Mar 16, 2022 at 7:43
  • @HandyHowie -- engine oil ?
    – amphibient
    Commented Mar 16, 2022 at 16:14
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    Yes, a little oil on the wire wool will help collect the removed rust in the wire wool.
    – HandyHowie
    Commented Mar 16, 2022 at 17:30

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It's not serious damage at this point but you definitely do not want to rotate the crankshaft and have the piston rings "clean" that off. Rust (i.e. iron oxide) is very abrasive and it will damage your rings.

As a first step I'd try to wipe of off with an oil soaked but otherwise clean rag. You'll want to get it out of the cylinder and not down into the space between the piston and the cylinder wall. If it's light surface rust, that should take care of it.

If that fails the next thing I'd try is a "scotchbrite" pad or, as HandyHowie mentioned, a steel wool pad. I prefer the scotchbrite type of pad as they leave behind fewer bits and pieces and tend to capture the stuff you are scrubbing off.

If the rust is worse than either of those will take care of, you might consider a cylinder hone of this type:

Flex Hone

Although in this case you will want to put something on top of the piston to catch any debris which will likely be a combination of removed rust and abrasive particles from the hone.

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