One problem related to noises during shifting has been reported for the 1998 Honda Civic. The most recently reported issues are listed below.
Since the day we bought it, the transmission intermittently jerked (sometimes violently) when downshifting, especially around 40 mph. It also downshifted at odd times, like going down hills. I took the car to the dealer on 12/12 & they reported "no problem found. " on Dec 27 the engine made lots of noise but had little speed & my family had to drive the handicapped car the short distance home. The dealer said the computer reported that the transmission ration was wrong. They said the more they worked on it, the worse it became. They couldn't fix it even with the help of Honda experts, so they intended to replaced the transmission. Unfortunately, the dealer wrecked the car & they have had the car a month. We want a new car because we don't trust the reliability of the car but Honda & the dealer aren't cooperating.