low and rough idle

About a week ago my water pump started leaking and I was too busy to fix it so I just kept adding water but it got worse the more I drove and one time after a long drive I started to get a rough crapy idle that sounds like its missing. I had the pump and belt replaced and the idle problem was still existant so I changed the plugs, distributor, ran injector cleaner and even cleaned the throttle body but nothing seems to fix this problem. See i have a drop in K&N filter with a big hole cut in the air box so my guess is water and coolant got into the intake. I idle just below the 800rpm mark but its a little smoother once am driving. Any suggestions??

95 xj 4x4 152,000 miles

Check your compression.