I have had the same problem with my 2000 Civic, with only 89k miles on it. I replaced the battery, made sure all the connections were good, and all that good stuff. Before I changed batteries, it idled at around 800 RPM, which is normal. After, its at like 200rpm, then it just dies. After about 10-15 minutes of it idling, it jumps back up to normal. I was told by a friend that the cars just reprogramming itself how to run. Its rather annoying..because at a redlight, I have to keep one foot on the brake, and on foot on the gas, just enough to keep it around 1k rpm, so it dosent die. But like I said...eventually it goes away, and idles normal....so it should be nothing to worry about.