1991 Ford Probe GT Cylinder Wall Rust

My roomate just recently acquired a 1991 Ford Probe GT 2.2l Turbo knowing that the cylinder head gasket was blown. The car had sat for quite a few months, my guess is at least 3+, and the cylinder walls
have rust present on them. I wouldn't consider them to be permanently damaged but there is significant spotting and it seems to have decent build up in some places. I haven't noticed any pits and I believe that a good cleaning with emory cloth might be the simple solution. The pistons have been sitting with a few ounces of motor oil on top of them for about 12 hours to lubricate the rings before we even attempted turning the crank. I think my next step is to remove the oil and soak them in a couple coats of WD-40 for a few hours, then attempt the scouring to remove the majority of the rust. I was just curious if this seems to be the logical way to proceed on this job and also to check and see how much of a surface imperfection on the cylinder wall could be tolerated before machining would be necessary.
Thanks for any tips, advice or suggestions!
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Was the engine stored with the head bolted in place ?
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The head was on the car, we just removed it last night and discovered the rust.
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Then the rust must have originated by condensation & your mentioned methods should work since the rust layer should be rather thin.
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