If the rust is only surface rust, just use wet and dry sandpaper with oil to remove the rust. Start with a 220 grit to remove the thicker rust, then follow with 320 and finer grits until smooth and shiny. Be aware that the ram surface should be well polished, almost to a mirror like finish. The use of a cloth polishing wheel is highly recommended for the final polishing.
Leaving the surface with a satin kind-of finish, or with rough surface is going to wear the seal sealing the ram faster. Also, and even worst, a non polished ram surface can grab the seal and twist it in its groove while going up or down, rendering it useless right away if it stays twisted or it might even break after some uses.
Same thing with the pump piston, if the seal is in a pump cylinder groove, polish the pump piston. If the seal is at the end of the pump piston, you need to polish the cylinder. Under
no circumstances you want a
cross etched pattern as the ones left by car engine hones. Every ram, pump piston and cylinder surface should be well polished with no scratches.
But before you start polishing you should check if a repair kit is available, as Hein Werner jacks more often than not use odd sizes for the seals and "generic" seals may not be available from aftermarket seal suppliers. Is a thing they did to force the owners to buy their kits instead of just buying a few seals from a local hydraulic shop, which should be cheaper and not a whole kit which should be more expensive. Still, you should measure the seals and contact your local hydraulic shop first to check availability, just to be sure.
Below see suppliers of repair kits.
http://www.hcrcnow.com/
http://www.blackhawkparts.com/page9.html
http://www.mcgivernhydraulics.com/