Ever since a huge rainfall 2 months ago the car runs very rough if I can even get it to start at all

Could use some more info on this, what year make and model of vehicle? Onw problem that I encountered was a misfire that wne ton for a while, turns out it was the dist. cap, even though the one I had looked good, as it was not even six months old, the #2 and #8 were arcing causing the misfire, reguardless of how new the cap is replace it, thats the first place to start, aside from making sure that you have all the wires properly attached ( proper firing order etc. )

I'm wondering if you could have a burnt exhaust valve cause by the exhaust leak in the cylinder where the exhaust leak was.

Since you have fuel injection for fuel delivery, something has to tell the system how long to have the fuel injectors open, and something has to tell the system when to activate each fuel injector ... unless you have throttle body injection. Do you know which type of fuel injection you have? I will need that answer above before telling you anything useful.

try replacing the throttle position sensor

Im having the same issue w/ my 99 maxima. had the problem 2 months ago, they replaced coil, changed plugs, told me that I would still get knock sensor code but dont worry about it. Now the rough idling and check light flashing is happening again.

pulls codes first auto zone checks for free

check the spark plug wires, put water in a spray bottle and spray along the wires,especially by the coil,if the car starts to run bad or you see sparks, the wires are no good, hope this helps, Ray

change your sparkplug wires that will salve yor problem

sounds like you have a huge vacuum leak at the engine, check under the hood for a sucking noise, I think you will find one.