I have a similular senerio as you...my engine was submerged in water but I have a snorkel on the intake so I never hydrolocked it. But I have been researching the problem for a bit and it seems that it has to so with "heat soak" which means when the engine gets to normal operational tempatures than shut off for about 10-15 mins exhaust flows back into the #3 cylinder and causes it to misfire. I have a check engine light on now I'm going to pull the code to make sure this is the problem, if I get it fixed I'll be sure to let you know!