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!