Hi guys, my first post here.

I got something funky going on with my civic but no one seems to have a clue what may be wrong with it. Here goes,

Three weeks ago I replaced plugs, fuel filter and wires and it was running real smooth.

About a week ago I ended driving tru some pretty deep puddle of water twice within about 5 minutes. Second time it happened my CEL immediately came on, and the engine started misfiring. It was still running, but rough as heck.
I pulled over right away and looked under the hood for any major water damage etc. Water was all over the place, but my car is bone stock. No CAI or anything. Some water got sucked thru a crack in the airbox cover , but it was minor.


So I managed to get my car looked at a local Autozone, and the guy pulled a P1399 code Random/multiple misfire. I went home and let the car dry out for about 6-8 hours.
Pulled the wires and plugs, made sure it was all dry, as well as distributor.

When I started it up again it ran just fine up till I hit 45 mph, when it started surging/hesitating/boggin down. It feels there's a damn jackhammer under the hood.
This lasts up untill I hit 65 mph, and afterwards it just smoothed itself out, like nothing is wrong with the engine. This happens regardless of engine speed.

I was wondering if anyone has an idea what to look for next. Someone suggested it's hydrolocked and bent a rod, but I seriously doubt that theory because car idles just fine and it's only that 45-65 mph window that's causing
problems. Another person suggested it's the ECU or maybe one of the sensors is shorted out. Possible problem with the injectors.

Please chime in if you have any idea what may be wrong, I'd greatly appreciate it.

 

Might wanna try a new dist cap. When water gets in there, the spark will take the path of least resistance to ground. Once it has found a new path to ground, it leaves a "carbon track" inside the dist cap. Once the carbon track has established itself (burns into the plastic) it very difficult to get rid of it. Sometimes you can see it, but it's very thin usually. I'd try drying it really good. If that doesn't help, replace it.

 

I would also make sure that the computer codes were cleared out. For a misfire from water, it doesnt have to actualy get into the distributor, just getting enough water ON the plug wires can cause it... especially with smaller plug wires. I have been offroading for years, and dont use anything less than 7mm plug wires. Standard wires can cause arcing when wet even with no cracks in the insulation.

Another thing to think about. WD40 displaces water. Keeping a tiny can handy somewhere in the car is a decent idea. Water could have gotten into ANY of the various plugs or connectors and possibly still causing a problem.... but that would be ky last thought.

You may also want to grab the rotor and ensure that the mechanical advance on the distributor is moving "freely"... not binding ir sticking.