Flash rust is actually a good thing- - -it means the block was cleaned well after boring/honing. I'd suggest giving the cylinders another good scrubdown with HOT water, laundry detergent, and a stiff-bristle scrub brush, then a boiling water rinse. Then give it a light coat of motor oil on a very clean rag to prevent further rusting before you assemble it. There's no such thing as cylinder walls that are too clean.
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
Cringe and wail in fear, Eloi- - - - -we Morlocks are on the hunt!
There is nothing noble in being superior to your fellow man; true nobility is being superior to your former self. - Ernest Hemingway
Love your enemies and drive 'em nuts!