It's not really going to be so great for the motor.. and likely, if your cyl walls have rust, I suspect that the rest of the motor also has some pretty significant damage.
My opinion would be that if you HAVE to do it this way... use one of those green pot scrubber pads and WD-40 to get as much of the loose surface rust off first. Then, if there is any significant amount left, use a brillo pad.
Whatever you do though, it's a good idea to have something protecting your pistons.. like... if you can find a plastic lid to a coffee can or something, see if you can find one that just fits in there.. you really don't want any of this stuff lodging itself into your rings when you finally start it up. At the VERY least.. put a rag in there at the bottom to catch the debris... your bearings are going to have a hard enough time as it is.
This of course goes without saying.. but make absolute sure that you empty all the oil out of your motor.. (there's probably water / milkshake consistency in there) and put 4 or 5 quarts of fresh 5W-30 motor oil in there (and a new filter). Do NOT.. ABSOLUTELY NOT put heavier weight oil in there. Our motors are not meant for it.. and in addition, your motor is going to take a LOT of wear on it's first startup having sat like this. You want good 30 weight oil... I would go with regular oil.. not synthetic.
Also, I would make sure that before you put the cyl head on.. your coat the walls of the cyls with some 5W-30 oil as well... it will help reduce the likely hood of damage to the rings when they make their first couple of passes.
Good luck... and make sure you change your oil and filter again after the first 30-40 miles... (don't skip this step)
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Todd,
2002 Ford Crown Victoria LX
1997 Pontiac Grand Am GT
1987 Pontiac Fiero SE / V6 5-Speed
1987 Pontiac Fiero SE / V6 (3.2L) Auto
1984 Pontiac Fiero 2m4 SE
1981 Pontiac TransAm (sbc 350)
1973 Volkswagen Type-2 Transporter