Over the past year, my engine would feel like its about to die with rpms going wild for maybe 2-5 seconds before returning to normal. This happened ONLY occasionally [like 3 times a month] while pulling out of driveways or shopping plazas onto the road.

Due to the fact the sometimes I was "climbing" onto the major road, I figured it might be something with fuel backflowing and taking some time to get to the engine. This was the only thing it could have imagined what caused this mystery. But the problem also occurred on flat surfaces as well. After pulling onto the road, it would sound like its almost dying for a couple of seconds before subsiding. It has happened in night and day, rain and sun.

........
Now what causes me to post is that I was driving maybe 1.5 hours through heavy rain in Atlanta this past weekend, and occasionally it was doing the same thing as before but on the freeway. The engine seemed like it was coughing almost for 5-10 seconds before picking back up. This happened at least 10 times in that 1.5 hours. Now I don’t know if water was getting into my cold air intake [its all the way down, but I still have the splash guard installed], or if it is related to the ongoing issue. But with the ongoing problem, it never happened while simply driving down the road. I'm thinking it was due to rain because its not happening now, but I dont know the answer to the ongoing problem.

So any ideas as to what is causing my ongoing problem?
Was it water that caused the problems this rainy weekend?
Any repercussions of water getting into intake? (car runs fine now, but im driving it easy)

1999 Accord Lx I4 automatic sedan with 100,000 miles
mods:exhaust, headers, intake [aem v2]
it has clean oil, timing belt was done 10k miles ago, air filter was cleaned and reoiled in the summer.

Hmm.....does it do that when you are driving with your AC on?

My lancer used to do that in the rain but its because I had no plastic covers on the bottom of the car, so when I would hit some water my belt would start slipping on a pulley, and my car was acting just like you have described.

now that you mention it, i did have on the AC this weekend in the rain. and when i cranked it up the next morning, the belts squealed for a second.

but when it randomly happens, i usually dont have on the AC.

I think the same belt runs your power steering too. Check you belt, see if it slacks a bit, or if its all ckacked up...if it is, then replace it ($15, 20 min worth of work).

On those 4-cyl F-series, the AC & alternator share a belt.
Power steering has it's own belt.

i had the drive belts replaced when i did the timing job. this was about 10k miles ago.

any other ideas?