The cylinder walls should have nothing on them... the rings scrape them clean every pass up and down.
The piston should only have possibly brown deposits of baked on oil (and not usually a whole lot of that).
I don't think you really gain anything by getting the brown spots off...but if you really "feel the need"... then steel wool sounds OK... but like you said... clean it all thoroughly before assembly.
If the cylinder and piston have evidence of seize marks and heavy scuffing... and I don't want to spend the money for a new piston and bore job..... then I will use 320 or 400 grit wet and dry sandpaper and put a light "cross hatch" sanding pattern on the scuffed spots... while wet sanding (with water).
"cross hatch" in the cylinder means side to side (not up and down like the piston travel).
Clean it thouroughly again.