1998 Other Hyundai Models running on 3 cylinders

Every time I hit a big puddle and water got anywhere near my engine, for a few seconds my car would run on 3 cylinders then run properly again. Now it is constantly on 3. I dont know if it is anything to do with the water because the day it stopped working completely it was dry outside. I have checked the HT leads and changed the spark plugs. I have replaced the manifold because there was a large crack in it, but it still doesnt work. It runs on 4 when I'm traveling at a steady speed keeping at the same RPM and it works well first thing in the morning when its cold. In the cat, the white stuff that looks like it should be round the outside has all fell down and looks like it may be blocking the exhaust? I dont know if that could be it.