If you're planning on honing the cylinders with the pistons installed, be aware that you'll need to get ALL the hone grit out of the cylinders afterwards. I once wore out a set of new piston rings on a cross-country trip from California to Tennessee to the point that after 2500 miles on a fresh "in the frame" rebuild, the engine was using 3 quarts of oil to a tank of gas. When we opened up the engine in Nashville, the oil ring expanders were rubbing the cylinder walls, and all the compression rings were half their original thickness. I had scrubbed the cylinders down after honing with clean rags and gasoline, followed by Lacquer thinner on clean paper towels until no stains were on the paper. Clean? I thought so! Now every cylinder I hone gets scrubbed down with hot soapy water and a stiff-bristle brush, and rinsed repeatedly with HOT water.
Use a button hone the proper size for your cylinders, powered by a 3/8" or 1/2" drill motor, lubricated liberally with 30 weight motor oil, and hone until the cylinder is smooth. You won't get rid of all the rust pits, but the surface where the rings ride will get smooth. If you can hang a fingernail in very many rust pits, it's time for a teardown and a rebore job.
Jerry