HondaCivicForum.com - Misfire help

Last night I had to drive through a pretty deep puddle (up to the doors). The car had to work to push through it and the engine bucked a couple times pretty hard. I think the clutch was slipping or something. By the time I got through the puddle, the engine had thrown a code and was running pretty rough. I figured I had soaked my air filter and I might be choking the enging, so I swung into the local parts shop and bought a new one just to be safe. That didn't fix the problem though. As I drove around more, the engine began to run better and would get brief bursts of it's normal self, but would then stumble again under load. This morning I drove about 25 minutes on the highway with no problem, but once I got off onto the surface streets it missed a couple more times. It's not a constant problem, but seems to show up when the engine is having to work. I'm wondering if I have a vacuum problem. Are there any lines on the bottom of the engine that may have been affected by driving through the water? Any other ideas? I thought maybe my dizzy had gotten wet, but I think that would be more of a constant problem. I'm at a loss, any clues? Thanks