What was the condition of the wires and plugs when you replaced them? Replaced them because of the # of miles or something was running poorly. By running poorly are you saying its missing? Or something else? Usually their is just a bit of oil from a bad valve cover gasket. To have water and rust means you must have been driving in deep water and have bad seals on the wires around the valve cover.
2001 ZX3 2.0L Zetec-
Hatch Nation #42
Going through Rebuild See "The TICK Build Thread" for details (http://www.focusfanatics.com/forum/showthread.php?t=289168&referrerid=62897)