I am in the middle of a rebuild and have my engine wrapped in plastic next to my car outside. Somehow, water happened to leak into some of the holes on top of the block. Small amounts of surface rust are on the bore, and the rod journals have a fair amount of rust. I need some kind of material that i can strip the rust off without damaging the bore or journals, and if the rust is bad enough on the journals, will i have to remachine them? crank still turns very smoothly and i was hoping i wouldnt have to break the bedplate seal to redo the crank. need help fast cause this has put a big damper on my rebuild.

you can try emery cloth. thats what machinists use i believe. as long as the rust isn't pitting you should be fine. you wont remove any material that would be considered an concern.

WD-40 and a rag. If it doesn't start to go away, try the emery cloth. If you are rubbing pretty hard, just take it to a machine shop and have it polished. Also put a set of bearings in the motor and bolt them down to spec and get a mic and check your clearances. Take that measurement to your machine shop so they know what they have to play with when they go to polish.

Just a tip- Emptying a can of WD-40 onto every single surface of a newly machined engine will prevent rust.