While I was in China the roof over the garage developed a leak near the chimney and leaked water over the lathe. Removing rust from a lathe bed is tricky because you cannot remove any metal or the lathe is no longer accurate. What I chose to use was phosphoric acid and a white scotch pad. Paper towels were cut to match the ways and then phosphoric acid was dripped onto them and allowed to set for 60 minutes. Then the paper towels were removed and the white scotch pad was used gently. It worked out well and between that and the bottoms of the tail piece, tool stay etc the lathe was fixed in less than a day. Fixing the ceiling took quite a bit longer and I did a temporary caulk job to hold until the roofer can come out for a permanent repair.

rusty lathe bed

cleaned rust from lathe